Changeset 3015 for trunk


Ignore:
Timestamp:
07/26/07 15:51:13 (13 years ago)
Author:
curtis
Message:

Add source code links to the Javadoc for every class.
I automated the insertion of these links, so please
let me know if you notice anything hosed up.

Location:
trunk/loci
Files:
373 edited

Legend:

Unmodified
Added
Removed
  • trunk/loci/apps/MultiLUT.java

    r2448 r3015  
    1717import java.rmi.RemoteException; 
    1818 
    19 /** An application for weighted spectral mapping. */ 
     19/** 
     20 * An application for weighted spectral mapping. 
     21 * 
     22 * <dl><dt><b>Source code:</b></dt> 
     23 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/apps/MultiLUT.java">Trac</a>, 
     24 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/apps/MultiLUT.java">SVN</a></dd></dl> 
     25 */ 
    2026public class MultiLUT extends Object implements ActionListener { 
    2127 
  • trunk/loci/apps/slim/SlimPlotter.java

    r2920 r3015  
    3737import visad.util.Util; 
    3838 
    39 /** A tool for visualization of spectral lifetime data. */ 
     39/** 
     40 * A tool for visualization of spectral lifetime data. 
     41 * 
     42 * <dl><dt><b>Source code:</b></dt> 
     43 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/apps/slim/SlimPlotter.java">Trac</a>, 
     44 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/apps/slim/SlimPlotter.java">SVN</a></dd></dl> 
     45 */ 
    4046public class SlimPlotter implements ActionListener, ChangeListener, 
    4147  DisplayListener, DocumentListener, Runnable, WindowListener 
  • trunk/loci/checks/About.java

    r1623 r3015  
    1212import javax.swing.JOptionPane; 
    1313 
    14 /** Displays a small information dialog about this package. */ 
     14/** 
     15 * Displays a small information dialog about this package. 
     16 * 
     17 * <dl><dt><b>Source code:</b></dt> 
     18 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/checks/About.java">Trac</a>, 
     19 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/checks/About.java">SVN</a></dd></dl> 
     20 */ 
    1521public final class About { 
    1622 
  • trunk/loci/checks/BlankLinesCheck.java

    r1619 r3015  
    1212import com.puppycrawl.tools.checkstyle.api.*; 
    1313 
    14 /** A Checkstyle check for identifying multiple consecutive blank lines. */ 
     14/** 
     15 * A Checkstyle check for identifying multiple consecutive blank lines. 
     16 * 
     17 * <dl><dt><b>Source code:</b></dt> 
     18 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/checks/BlankLinesCheck.java">Trac</a>, 
     19 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/checks/BlankLinesCheck.java">SVN</a></dd></dl> 
     20 */ 
    1521public class BlankLinesCheck extends Check { 
    1622 
  • trunk/loci/formats/AggregateMetadataStore.java

    r2455 r3015  
    3232 * A metadata store which delegates the actual storage to one or more <i>sub</i> 
    3333 * metadata stores. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/AggregateMetadataStore.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/AggregateMetadataStore.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Chris Allan callan at blackcat.ca 
  • trunk/loci/formats/AxisGuesser.java

    r2857 r3015  
    3232 * dimensional axes (Z, T or C), potentially recommending an adjustment in 
    3333 * dimension order within the files, depending on the confidence of each guess. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/AxisGuesser.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/AxisGuesser.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/ChannelMerger.java

    r2796 r3015  
    2828import java.io.*; 
    2929 
    30 /** Logic to automatically merge channels in a file. */ 
     30/** 
     31 * Logic to automatically merge channels in a file. 
     32 * 
     33 * <dl><dt><b>Source code:</b></dt> 
     34 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ChannelMerger.java">Trac</a>, 
     35 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ChannelMerger.java">SVN</a></dd></dl> 
     36 */ 
    3137public class ChannelMerger extends ReaderWrapper { 
    3238 
  • trunk/loci/formats/ChannelSeparator.java

    r2976 r3015  
    2828import java.io.IOException; 
    2929 
    30 /** Logic to automatically separate the channels in a file. */ 
     30/** 
     31 * Logic to automatically separate the channels in a file. 
     32 * 
     33 * <dl><dt><b>Source code:</b></dt> 
     34 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ChannelSeparator.java">Trac</a>, 
     35 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ChannelSeparator.java">SVN</a></dd></dl> 
     36 */ 
    3137public class ChannelSeparator extends ReaderWrapper { 
    3238 
  • trunk/loci/formats/ClassList.java

    r3011 r3015  
    3333 * ClassList is a list of classes for use with ImageReader or ImageWriter, 
    3434 * parsed from a configuration file such as readers.txt or writers.txt. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ClassList.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ClassList.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/ConsoleTools.java

    r3013 r3015  
    3232import java.util.Hashtable; 
    3333 
    34 /** A utility class for command line tools. */ 
     34/** 
     35 * A utility class for command line tools. 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ConsoleTools.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ConsoleTools.java">SVN</a></dd></dl> 
     40 */ 
    3541public final class ConsoleTools { 
    3642 
     
    570576    LogTools.print(in + " "); 
    571577    ImageReader reader = new ImageReader(); 
    572     reader.setOriginalMetadataPopulated(true);  
     578    reader.setOriginalMetadataPopulated(true); 
    573579 
    574580    try { 
     
    577583      reader.setMetadataStore(ms); 
    578584    } 
    579     catch (Throwable t) {  
    580       LogTools.println("OME-Java library not found.");  
     585    catch (Throwable t) { 
     586      LogTools.println("OME-Java library not found."); 
    581587    } 
    582588 
    583589    reader.setId(in); 
    584590    LogTools.print("[" + reader.getFormat() + "] -> " + out + " "); 
    585      
    586     MetadataStore store = reader.getMetadataStore();  
     591 
     592    MetadataStore store = reader.getMetadataStore(); 
    587593    if (store instanceof MetadataRetrieve) { 
    588594      writer.setMetadataRetrieve((MetadataRetrieve) store); 
  • trunk/loci/formats/CoreMetadata.java

    r2768 r3015  
    2727import java.util.Hashtable; 
    2828 
    29 /** Encompasses core metadata values. */ 
     29/** 
     30 * Encompasses core metadata values. 
     31 * 
     32 * <dl><dt><b>Source code:</b></dt> 
     33 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/CoreMetadata.java">Trac</a>, 
     34 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/CoreMetadata.java">SVN</a></dd></dl> 
     35 */ 
    3036public class CoreMetadata { 
    3137  public int[] sizeX, sizeY, sizeZ, sizeC, sizeT; 
  • trunk/loci/formats/DataTools.java

    r3012 r3015  
    3232 * A utility class with convenience methods for 
    3333 * reading, writing and decoding words. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/DataTools.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/DataTools.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Curtis Rueden ctrueden at wisc.edu 
     
    522526 
    523527  // -- Date handling -- 
    524    
     528 
    525529  /** Converts the given timestamp into an ISO 8061 date. */ 
    526530  public static String convertDate(long stamp, int format) { 
     
    542546 
    543547    fmt.format(d, sb, new FieldPosition(0)); 
    544     return sb.toString();  
     548    return sb.toString(); 
    545549  } 
    546550 
  • trunk/loci/formats/DimensionSwapper.java

    r2701 r3015  
    2525package loci.formats; 
    2626 
    27 /** Handles swapping the dimension order of a file. */ 
     27/** 
     28 * Handles swapping the dimension order of a file. 
     29 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/DimensionSwapper.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/DimensionSwapper.java">SVN</a></dd></dl> 
     33 */ 
    2834public class DimensionSwapper extends ReaderWrapper { 
    2935 
  • trunk/loci/formats/DummyMetadataStore.java

    r2320 r3015  
    2828 * A dummy <code>MetadataStore</code> implementation that is used when no other 
    2929 * metadata stores are available. 
     30 * 
     31 * <dl><dt><b>Source code:</b></dt> 
     32 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/DummyMetadataStore.java">Trac</a>, 
     33 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/DummyMetadataStore.java">SVN</a></dd></dl> 
    3034 * 
    3135 * @author Chris Allan callan at blackcat.ca 
  • trunk/loci/formats/FilePattern.java

    r2857 r3015  
    4141 *   <li>/data/Josiah/cell-Z&lt;0-39&gt;.C&lt;0-1&gt;.tiff</li> 
    4242 * </ul> 
     43 * 
     44 * <dl><dt><b>Source code:</b></dt> 
     45 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/FilePattern.java">Trac</a>, 
     46 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/FilePattern.java">SVN</a></dd></dl> 
    4347 * 
    4448 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/FileStitcher.java

    r2998 r3015  
    3333 * Logic to stitch together files with similar names. 
    3434 * Assumes that all files have the same dimensions. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/FileStitcher.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/FileStitcher.java">SVN</a></dd></dl> 
    3539 */ 
    3640public class FileStitcher implements IFormatReader { 
  • trunk/loci/formats/FormatException.java

    r2178 r3015  
    2828 * FormatException is the exception thrown when something 
    2929 * goes wrong performing a file format operation. 
     30 * 
     31 * <dl><dt><b>Source code:</b></dt> 
     32 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/FormatException.java">Trac</a>, 
     33 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/FormatException.java">SVN</a></dd></dl> 
    3034 */ 
    3135public class FormatException extends Exception { 
  • trunk/loci/formats/FormatHandler.java

    r2857 r3015  
    2828import java.util.Vector; 
    2929 
    30 /** Abstract superclass of all biological file format readers and writers. */ 
     30/** 
     31 * Abstract superclass of all biological file format readers and writers. 
     32 * 
     33 * <dl><dt><b>Source code:</b></dt> 
     34 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/FormatHandler.java">Trac</a>, 
     35 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/FormatHandler.java">SVN</a></dd></dl> 
     36 */ 
    3137public abstract class FormatHandler implements IFormatHandler { 
    3238 
  • trunk/loci/formats/FormatReader.java

    r2998 r3015  
    3030import java.util.*; 
    3131 
    32 /** Abstract superclass of all biological file format readers. */ 
     32/** 
     33 * Abstract superclass of all biological file format readers. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/FormatReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/FormatReader.java">SVN</a></dd></dl> 
     38 */ 
    3339public abstract class FormatReader extends FormatHandler 
    3440  implements IFormatReader 
  • trunk/loci/formats/FormatTools.java

    r3013 r3015  
    2727import java.util.StringTokenizer; 
    2828 
    29 /** A utility class for format reader and writer implementations. */ 
     29/** 
     30 * A utility class for format reader and writer implementations. 
     31 * 
     32 * <dl><dt><b>Source code:</b></dt> 
     33 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/FormatTools.java">Trac</a>, 
     34 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/FormatTools.java">SVN</a></dd></dl> 
     35 */ 
    3036public final class FormatTools { 
    3137 
     
    449455  // -- Utility methods -- metadata conversion -- 
    450456 
    451   public static void convertMetadata(MetadataRetrieve source,  
     457  public static void convertMetadata(MetadataRetrieve source, 
    452458    MetadataStore dest) 
    453459  { 
     
    455461    int globalPixCount = 0; 
    456462 
    457     for (int i=0; i<source.getImageCount(); i++) {   
    458       ii = new Integer(i);  
     463    for (int i=0; i<source.getImageCount(); i++) { 
     464      ii = new Integer(i); 
    459465      dest.setImage(source.getImageName(ii), source.getCreationDate(ii), 
    460466        source.getDescription(ii), ii); 
    461      
    462       dest.setDimensions(source.getPixelSizeX(ii),  
     467 
     468      dest.setDimensions(source.getPixelSizeX(ii), 
    463469        source.getPixelSizeY(ii), source.getPixelSizeZ(ii), 
    464470        source.getPixelSizeC(ii), source.getPixelSizeT(ii), ii); 
    465      
     471 
    466472      for (int j=0; j<source.getPixelsCount(ii); j++) { 
    467         Integer p = new Integer(j);  
     473        Integer p = new Integer(j); 
    468474        dest.setPixels(source.getSizeX(ii), source.getSizeY(ii), 
    469           source.getSizeZ(ii), source.getSizeC(ii),  
    470           source.getSizeT(ii),  
    471           new Integer(pixelTypeFromString(source.getPixelType(ii))),  
     475          source.getSizeZ(ii), source.getSizeC(ii), 
     476          source.getSizeT(ii), 
     477          new Integer(pixelTypeFromString(source.getPixelType(ii))), 
    472478          source.getBigEndian(ii), source.getDimensionOrder(ii), ii, p); 
    473     
     479 
    474480        dest.setDisplayOptions(source.getZoom(ii), 
    475481          source.isRedChannelOn(ii), source.isGreenChannelOn(ii), 
     
    484490          Integer c = new Integer(ch); 
    485491          dest.setLogicalChannel(ch, source.getChannelName(globalPix, c), 
    486             source.getChannelNDFilter(globalPix, c),  
     492            source.getChannelNDFilter(globalPix, c), 
    487493            source.getEmWave(globalPix, c), source.getExWave(globalPix, c), 
    488494            source.getPhotometricInterpretation(globalPix, c), 
    489495            source.getMode(globalPix, c), globalPix); 
    490          
     496 
    491497          dest.setChannelGlobalMinMax(ch, source.getGlobalMin(globalPix, c), 
    492498            source.getGlobalMax(globalPix, c), globalPix); 
    493          
     499 
    494500          dest.setDisplayChannel(c, source.getBlackLevel(globalPix, c), 
    495             source.getWhiteLevel(globalPix, c), source.getGamma(globalPix, c),  
     501            source.getWhiteLevel(globalPix, c), source.getGamma(globalPix, c), 
    496502            globalPix); 
    497         }  
    498  
    499         globalPixCount++;  
     503        } 
     504 
     505        globalPixCount++; 
    500506      } 
    501    
     507 
    502508      dest.setImagingEnvironment(source.getTemperature(ii), 
    503509        source.getAirPressure(ii), source.getHumidity(ii), 
     
    506512 
    507513    for (int i=0; i<source.getExperimenterCount(); i++) { 
    508       ii = new Integer(i);  
    509       dest.setExperimenter(source.getFirstName(ii),  
     514      ii = new Integer(i); 
     515      dest.setExperimenter(source.getFirstName(ii), 
    510516        source.getLastName(ii), source.getEmail(ii), 
    511517        source.getInstitution(ii), source.getDataDirectory(ii), 
     
    514520 
    515521    for (int i=0; i<source.getGroupCount(); i++) { 
    516       ii = new Integer(i);  
     522      ii = new Integer(i); 
    517523      dest.setGroup(source.getGroupName(ii), source.getLeader(ii), 
    518524        source.getContact(ii), ii); 
     
    520526 
    521527    for (int i=0; i<source.getInstrumentCount(); i++) { 
    522       ii = new Integer(i);  
     528      ii = new Integer(i); 
    523529      dest.setInstrument(source.getManufacturer(ii), 
    524530        source.getModel(ii), source.getSerialNumber(ii), 
     
    527533 
    528534    for (int i=0; i<source.getDisplayROICount(); i++) { 
    529       ii = new Integer(i);  
     535      ii = new Integer(i); 
    530536      dest.setDisplayROI(source.getX0(ii), source.getY0(ii), 
    531537        source.getZ0(ii), source.getX1(ii), source.getY1(ii), 
     
    534540    } 
    535541 
    536     for (int i=0; i<source.getStageLabelCount(); i++) {  
    537       ii = new Integer(i);  
     542    for (int i=0; i<source.getStageLabelCount(); i++) { 
     543      ii = new Integer(i); 
    538544      dest.setStageLabel(source.getStageName(ii), source.getStageX(ii), 
    539545        source.getStageY(ii), source.getStageZ(ii), ii); 
     
    565571 
    566572    dest.setObjective(source.getObjectiveManufacturer(ii), 
    567       source.getObjectiveModel(ii), source.getObjectiveSerial(ii),  
     573      source.getObjectiveModel(ii), source.getObjectiveSerial(ii), 
    568574      source.getLensNA(ii), 
    569575      source.getObjectiveMagnification(ii), ii, ii); 
     
    581587 
    582588    dest.setFilterSet(source.getFilterSetManufacturer(ii), 
    583       source.getFilterSetModel(ii),  
     589      source.getFilterSetModel(ii), 
    584590      source.getFilterSetLotNumber(ii), ii, ii); 
    585591 
  • trunk/loci/formats/FormatWriter.java

    r3013 r3015  
    2929import java.io.IOException; 
    3030 
    31 /** Abstract superclass of all biological file format writers. */ 
     31/** 
     32 * Abstract superclass of all biological file format writers. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/FormatWriter.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/FormatWriter.java">SVN</a></dd></dl> 
     37 */ 
    3238public abstract class FormatWriter extends FormatHandler 
    3339  implements IFormatWriter 
     
    7379 
    7480  /* @see IFormatWriter#saveBytes(byte[], int, boolean, boolean) */ 
    75   public void saveBytes(byte[] bytes, int series, boolean lastInSeries,  
     81  public void saveBytes(byte[] bytes, int series, boolean lastInSeries, 
    7682    boolean last) throws FormatException, IOException 
    7783  { 
     
    8086 
    8187  /* @see IFormatWriter#saveImage(Image, int, boolean, boolean) */ 
    82   public void saveImage(Image image, int series, boolean lastInSeries,  
     88  public void saveImage(Image image, int series, boolean lastInSeries, 
    8389    boolean last) throws FormatException, IOException 
    8490  { 
  • trunk/loci/formats/IFormatHandler.java

    r2687 r3015  
    2727import java.io.IOException; 
    2828 
    29 /** Interface for all biological file format readers and writers. */ 
     29/** 
     30 * Interface for all biological file format readers and writers. 
     31 * 
     32 * <dl><dt><b>Source code:</b></dt> 
     33 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/IFormatHandler.java">Trac</a>, 
     34 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/IFormatHandler.java">SVN</a></dd></dl> 
     35 */ 
    3036public interface IFormatHandler extends StatusReporter { 
    3137 
  • trunk/loci/formats/IFormatReader.java

    r2998 r3015  
    2929import java.util.Hashtable; 
    3030 
    31 /** Interface for all biological file format readers. */ 
     31/** 
     32 * Interface for all biological file format readers. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/IFormatReader.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/IFormatReader.java">SVN</a></dd></dl> 
     37 */ 
    3238public interface IFormatReader extends IFormatHandler { 
    3339 
  • trunk/loci/formats/IFormatWriter.java

    r3013 r3015  
    2929import java.io.IOException; 
    3030 
    31 /** Interface for all biological file format writers. */ 
     31/** 
     32 * Interface for all biological file format writers. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/IFormatWriter.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/IFormatWriter.java">SVN</a></dd></dl> 
     37 */ 
    3238public interface IFormatWriter extends IFormatHandler { 
    3339 
     
    4450   * If this image is the last one in the file, the last flag must be set. 
    4551   */ 
    46   void saveImage(Image image, int series, boolean lastInSeries, boolean last)  
     52  void saveImage(Image image, int series, boolean lastInSeries, boolean last) 
    4753    throws FormatException, IOException; 
    4854 
  • trunk/loci/formats/IRandomAccess.java

    r2455 r3015  
    2929/** 
    3030 * Interface for random access into structures (e.g., files or arrays). 
     31 * 
     32 * <dl><dt><b>Source code:</b></dt> 
     33 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/IRandomAccess.java">Trac</a>, 
     34 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/IRandomAccess.java">SVN</a></dd></dl> 
    3135 * 
    3236 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/ImageReader.java

    r2998 r3015  
    3333 * It uses one instance of each reader subclass (specified in readers.txt, 
    3434 * or other class list source) to identify file formats and read data. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ImageReader.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ImageReader.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/ImageTools.java

    r2976 r3015  
    3535 * Much code was stolen and adapted from DrLaszloJamf's posts at: 
    3636 *   http://forum.java.sun.com/thread.jspa?threadID=522483 
     37 * 
     38 * <dl><dt><b>Source code:</b></dt> 
     39 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ImageTools.java">Trac</a>, 
     40 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ImageTools.java">SVN</a></dd></dl> 
    3741 * 
    3842 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/ImageWriter.java

    r3013 r3015  
    3434 * It uses one instance of each writer subclass (specified in writers.txt, 
    3535 * or other class list source) to identify file formats and write data. 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ImageWriter.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ImageWriter.java">SVN</a></dd></dl> 
    3640 * 
    3741 * @author Curtis Rueden ctrueden at wisc.edu 
     
    171175 
    172176  /* @see IFormatWriter#saveBytes(byte[], int, boolean, boolean) */ 
    173   public void saveBytes(byte[] bytes, int series, boolean lastInSeries,  
     177  public void saveBytes(byte[] bytes, int series, boolean lastInSeries, 
    174178    boolean last) throws FormatException, IOException 
    175179  { 
    176180    getWriter().saveBytes(bytes, series, lastInSeries, last); 
    177   }  
     181  } 
    178182 
    179183  /* @see IFormatWriter#saveImage(Image, boolean) */ 
     
    185189 
    186190  /* @see IFormatWriter#saveImage(Image, int, boolean, boolean) */ 
    187   public void saveImage(Image image, int series, boolean lastInSeries,  
     191  public void saveImage(Image image, int series, boolean lastInSeries, 
    188192    boolean last) throws FormatException, IOException 
    189193  { 
  • trunk/loci/formats/LegacyQTTools.java

    r2857 r3015  
    3131import java.util.StringTokenizer; 
    3232 
    33 /** Utility class for working with QuickTime for Java. */ 
     33/** 
     34 * Utility class for working with QuickTime for Java. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/LegacyQTTools.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/LegacyQTTools.java">SVN</a></dd></dl> 
     39 */ 
    3440public class LegacyQTTools { 
    3541 
  • trunk/loci/formats/Location.java

    r2494 r3015  
    3333 * Pseudo-extension of java.io.File that supports reading over HTTP. 
    3434 * It is strongly recommended that you use this instead of java.io.File. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/Location.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/Location.java">SVN</a></dd></dl> 
    3539 */ 
    3640public class Location { 
  • trunk/loci/formats/Log.java

    r3002 r3015  
    2828import java.io.PrintStream; 
    2929 
    30 /** A simple logging class. */ 
     30/** 
     31 * A simple logging class. 
     32 * 
     33 * <dl><dt><b>Source code:</b></dt> 
     34 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/Log.java">Trac</a>, 
     35 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/Log.java">SVN</a></dd></dl> 
     36 */ 
    3137public class Log { 
    3238 
  • trunk/loci/formats/LogTools.java

    r2857 r3015  
    2525package loci.formats; 
    2626 
    27 /** A utility class for logging. */ 
     27/** 
     28 * A utility class for logging. 
     29 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/LogTools.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/LogTools.java">SVN</a></dd></dl> 
     33 */ 
    2834public final class LogTools { 
    2935 
  • trunk/loci/formats/MetadataRetrieve.java

    r3013 r3015  
    6060  /** 
    6161   * Gets the first name of the nth experimenter. 
    62    * @param n the index of the experimenter.  If <code>null</code> the default  
     62   * @param n the index of the experimenter.  If <code>null</code> the default 
    6363   * index of 0 will be used. 
    6464   */ 
     
    6767  /** 
    6868   * Gets the last name of the nth experimenter. 
    69    * @param n the index of the experimenter.  If <code>null</code> the default  
     69   * @param n the index of the experimenter.  If <code>null</code> the default 
    7070   * index of 0 will be used. 
    7171   */ 
     
    7474  /** 
    7575   * Gets the email address of the nth experimenter. 
    76    * @param n the index of the experimenter.  If <code>null</code> the default  
     76   * @param n the index of the experimenter.  If <code>null</code> the default 
    7777   * index of 0 will be used. 
    7878   */ 
     
    8181  /** 
    8282   * Gets the institution of the nth experimenter. 
    83    * @param n the index of the experimenter.  If <code>null</code> the default  
     83   * @param n the index of the experimenter.  If <code>null</code> the default 
    8484   * index of 0 will be used. 
    8585   */ 
     
    8888  /** 
    8989   * Gets the data directory of the nth experimenter. 
    90    * @param n the index of the experimenter.  If <code>null</code> the default  
     90   * @param n the index of the experimenter.  If <code>null</code> the default 
    9191   * index of 0 will be used. 
    9292   */ 
     
    9595  /** 
    9696   * Gets the group of the nth experimenter. 
    97    * @param n the index of the experimenter.  If <code>null</code> the default  
     97   * @param n the index of the experimenter.  If <code>null</code> the default 
    9898   * index of 0 will be used. 
    9999   */ 
     
    101101 
    102102  // -- Group attribute retrieval methods -- 
    103   
     103 
    104104  /** Returns the number of groups. */ 
    105105  int getGroupCount(); 
     
    107107  /** 
    108108   * Get the name of the nth group. 
    109    * @param n the index of the group.  If <code>null</code> the default  
     109   * @param n the index of the group.  If <code>null</code> the default 
    110110   * index of 0 will be used. 
    111111   */ 
     
    114114  /** 
    115115   * Get the leader of the nth group. 
    116    * @param n the index of the group.  If <code>null</code> the default  
     116   * @param n the index of the group.  If <code>null</code> the default 
    117117   * index of 0 will be used. 
    118118   */ 
     
    121121  /** 
    122122   * Get the contact of the nth group. 
    123    * @param n the index of the group.  If <code>null</code> the default  
     123   * @param n the index of the group.  If <code>null</code> the default 
    124124   * index of 0 will be used. 
    125125   */ 
     
    133133  /** 
    134134   * Get the manufacturer of the nth instrument. 
    135    * @param n the index of the instrument.  If <code>null</code> the default  
     135   * @param n the index of the instrument.  If <code>null</code> the default 
    136136   * index of 0 will be used. 
    137137   */ 
     
    140140  /** 
    141141   * Get the model of the nth instrument. 
    142    * @param n the index of the instrument.  If <code>null</code> the default  
     142   * @param n the index of the instrument.  If <code>null</code> the default 
    143143   * index of 0 will be used. 
    144144   */ 
     
    147147  /** 
    148148   * Get the serial number of the nth instrument. 
    149    * @param n the index of the instrument.  If <code>null</code> the default  
     149   * @param n the index of the instrument.  If <code>null</code> the default 
    150150   * index of 0 will be used. 
    151151   */ 
     
    154154  /** 
    155155   * Get the type of the nth instrument. 
    156    * @param n the index of the instrument.  If <code>null</code> the default  
     156   * @param n the index of the instrument.  If <code>null</code> the default 
    157157   * index of 0 will be used. 
    158158   */ 
     
    203203  /** 
    204204   * Get the lower X bound of the nth ROI. 
    205    * @param n the index of the ROI.  If <code>null</code> the default  
     205   * @param n the index of the ROI.  If <code>null</code> the default 
    206206   * index of 0 will be used. 
    207207   */ 
     
    210210  /** 
    211211   * Get the lower Y bound of the nth ROI. 
    212    * @param n the index of the ROI.  If <code>null</code> the default  
     212   * @param n the index of the ROI.  If <code>null</code> the default 
    213213   * index of 0 will be used. 
    214214   */ 
     
    217217  /** 
    218218   * Get the lower Z bound of the nth ROI. 
    219    * @param n the index of the ROI.  If <code>null</code> the default  
     219   * @param n the index of the ROI.  If <code>null</code> the default 
    220220   * index of 0 will be used. 
    221221   */ 
     
    224224  /** 
    225225   * Get the lower T bound of the nth ROI. 
    226    * @param n the index of the ROI.  If <code>null</code> the default  
     226   * @param n the index of the ROI.  If <code>null</code> the default 
    227227   * index of 0 will be used. 
    228228   */ 
     
    231231  /** 
    232232   * Get the upper X bound of the nth ROI. 
    233    * @param n the index of the ROI.  If <code>null</code> the default  
     233   * @param n the index of the ROI.  If <code>null</code> the default 
    234234   * index of 0 will be used. 
    235235   */ 
     
    238238  /** 
    239239   * Get the upper Y bound of the nth ROI. 
    240    * @param n the index of the ROI.  If <code>null</code> the default  
     240   * @param n the index of the ROI.  If <code>null</code> the default 
    241241   * index of 0 will be used. 
    242242   */ 
     
    245245  /** 
    246246   * Get the upper Z bound of the nth ROI. 
    247    * @param n the index of the ROI.  If <code>null</code> the default  
     247   * @param n the index of the ROI.  If <code>null</code> the default 
    248248   * index of 0 will be used. 
    249249   */ 
     
    252252  /** 
    253253   * Get the upper T bound of the nth ROI. 
    254    * @param n the index of the ROI.  If <code>null</code> the default  
     254   * @param n the index of the ROI.  If <code>null</code> the default 
    255255   * index of 0 will be used. 
    256256   */ 
     
    259259  /** 
    260260   * Get the display options of the nth ROI. 
    261    * @param n the index of the ROI.  If <code>null</code> the default  
     261   * @param n the index of the ROI.  If <code>null</code> the default 
    262262   * index of 0 will be used. 
    263263   */ 
     
    271271  /** 
    272272   * Gets the SizeX attribute of the given pixels in the given image. 
    273    * @param image the index of the image.  If <code>null</code> the default  
     273   * @param image the index of the image.  If <code>null</code> the default 
    274274   * index of 0 will be used. 
    275275   */ 
    276276  Integer getSizeX(Integer image); 
    277    
     277 
    278278  /** 
    279279   * Gets the SizeY attribute of the given pixels in the given image. 
    280    * @param image the index of the image.  If <code>null</code> the default  
     280   * @param image the index of the image.  If <code>null</code> the default 
    281281   * index of 0 will be used. 
    282282   */ 
     
    285285  /** 
    286286   * Gets the SizeZ attribute of the given pixels in the given image. 
    287    * @param image the index of the image.  If <code>null</code> the default  
     287   * @param image the index of the image.  If <code>null</code> the default 
    288288   * index of 0 will be used. 
    289289   */ 
     
    292292  /** 
    293293   * Gets the SizeC attribute of the given pixels in the given image. 
    294    * @param image the index of the image.  If <code>null</code> the default  
     294   * @param image the index of the image.  If <code>null</code> the default 
    295295   * index of 0 will be used. 
    296296   */ 
     
    299299  /** 
    300300   * Gets the SizeT attribute of the given pixels in the given image. 
    301    * @param image the index of the image.  If <code>null</code> the default  
     301   * @param image the index of the image.  If <code>null</code> the default 
    302302   * index of 0 will be used. 
    303303   */ 
     
    306306  /** 
    307307   * Gets the PixelType attribute of the given pixels in the given image. 
    308    * @param image the index of the image.  If <code>null</code> the default  
     308   * @param image the index of the image.  If <code>null</code> the default 
    309309   * index of 0 will be used. 
    310310   */ 
     
    313313  /** 
    314314   * Gets the BigEndian attribute of the given pixels in the given image. 
    315    * @param image the index of the image.  If <code>null</code> the default  
     315   * @param image the index of the image.  If <code>null</code> the default 
    316316   * index of 0 will be used. 
    317317   */ 
     
    320320  /** 
    321321   * Gets the DimensionOrder attribute of the given pixels in the given image. 
    322    * @param image the index of the image.  If <code>null</code> the default  
     322   * @param image the index of the image.  If <code>null</code> the default 
    323323   * index of 0 will be used. 
    324324   */ 
     
    372372  String getChannelName(Integer pixels, Integer channel); 
    373373 
    374   /**  
    375    * Gets the ND filter value for the given channel in the given set of pixels.  
    376    * @param pixels the index of the pixels.  If <code>null</code> the default 
    377    * index of 0 will be used. 
    378    * @param channel the index of the channel.  If <code>null</code> the default 
    379    * index of 0 will be used. 
    380    */  
     374  /** 
     375   * Gets the ND filter value for the given channel in the given set of pixels. 
     376   * @param pixels the index of the pixels.  If <code>null</code> the default 
     377   * index of 0 will be used. 
     378   * @param channel the index of the channel.  If <code>null</code> the default 
     379   * index of 0 will be used. 
     380   */ 
    381381  Float getChannelNDFilter(Integer pixels, Integer channel); 
    382382 
    383383  /** 
    384    * Gets the emission wavelength of the given channel in the given  
     384   * Gets the emission wavelength of the given channel in the given 
    385385   * set of pixels. 
    386386   * @param pixels the index of the pixels.  If <code>null</code> the default 
     
    421421 
    422422  /** 
    423    * Gets the minimum pixel value within the given channel in the  
     423   * Gets the minimum pixel value within the given channel in the 
    424424   * given set of pixels. 
    425425   * @param pixels the index of the pixels.  If <code>null</code> the default 
     
    431431 
    432432  /** 
    433    * Gets the maximum pixel value within the given channel in the  
     433   * Gets the maximum pixel value within the given channel in the 
    434434   * given set of pixels. 
    435435   * @param pixels the index of the pixels.  If <code>null</code> the default 
     
    457457 
    458458  /** 
    459    * Gets the exposure time of the plane with the given Z, C and T coordinates  
     459   * Gets the exposure time of the plane with the given Z, C and T coordinates 
    460460   * in the given set of pixels. 
    461461   * @param pixels the index of the pixels.  If <code>null</code> the default 
     
    504504  /** 
    505505   * Gets the black level of the given channel in the given set of pixels. 
    506    * @param pixels the index of the pixels.  If <code>null</code> the default  
    507    * index of 0 will be used. 
    508    * @param channel the index of the channel.  If <code>null</code> the default  
    509    * index of 0 will be used. 
    510    */  
     506   * @param pixels the index of the pixels.  If <code>null</code> the default 
     507   * index of 0 will be used. 
     508   * @param channel the index of the channel.  If <code>null</code> the default 
     509   * index of 0 will be used. 
     510   */ 
    511511  Double getBlackLevel(Integer pixels, Integer channel); 
    512512 
    513513  /** 
    514514   * Gets the white level of the given channel in the given set of pixels. 
    515    * @param pixels the index of the pixels.  If <code>null</code> the default  
    516    * index of 0 will be used. 
    517    * @param channel the index of the channel.  If <code>null</code> the default  
    518    * index of 0 will be used. 
    519    */  
     515   * @param pixels the index of the pixels.  If <code>null</code> the default 
     516   * index of 0 will be used. 
     517   * @param channel the index of the channel.  If <code>null</code> the default 
     518   * index of 0 will be used. 
     519   */ 
    520520  Double getWhiteLevel(Integer pixels, Integer channel); 
    521521 
    522522  /** 
    523523   * Gets the gamma value of the given channel in the given set of pixels. 
    524    * @param pixels the index of the pixels.  If <code>null</code> the default  
    525    * index of 0 will be used. 
    526    * @param channel the index of the channel.  If <code>null</code> the default  
    527    * index of 0 will be used. 
    528    */  
     524   * @param pixels the index of the pixels.  If <code>null</code> the default 
     525   * index of 0 will be used. 
     526   * @param channel the index of the channel.  If <code>null</code> the default 
     527   * index of 0 will be used. 
     528   */ 
    529529  Float getGamma(Integer pixels, Integer channel); 
    530530 
     
    532532 
    533533  /** 
    534    * Gets the zoom value associated with the given pixels in the given image.  
    535    * @param image the index of the image.  If <code>null</code> the default  
    536    * index of 0 will be used. 
    537    */  
     534   * Gets the zoom value associated with the given pixels in the given image. 
     535   * @param image the index of the image.  If <code>null</code> the default 
     536   * index of 0 will be used. 
     537   */ 
    538538  Float getZoom(Integer image); 
    539539 
    540540  /** 
    541541   * Gets whether or not the red channel is activated. 
    542    * @param image the index of the image.  If <code>null</code> the default  
    543    * index of 0 will be used. 
    544    */  
     542   * @param image the index of the image.  If <code>null</code> the default 
     543   * index of 0 will be used. 
     544   */ 
    545545  Boolean isRedChannelOn(Integer image); 
    546546 
    547547  /** 
    548548   * Gets whether or not the green channel is activated. 
    549    * @param image the index of the image.  If <code>null</code> the default  
    550    * index of 0 will be used. 
    551    */  
     549   * @param image the index of the image.  If <code>null</code> the default 
     550   * index of 0 will be used. 
     551   */ 
    552552  Boolean isGreenChannelOn(Integer image); 
    553553 
    554554  /** 
    555555   * Gets whether or not the blue channel is activated. 
    556    * @param image the index of the image.  If <code>null</code> the default  
    557    * index of 0 will be used. 
    558    */  
     556   * @param image the index of the image.  If <code>null</code> the default 
     557   * index of 0 will be used. 
     558   */ 
    559559  Boolean isBlueChannelOn(Integer image); 
    560560 
    561561  /** 
    562562   * Gets whether or not the given pixels are displayed as an RGB image. 
    563    * @param image the index of the image.  If <code>null</code> the default  
    564    * index of 0 will be used. 
    565    */  
     563   * @param image the index of the image.  If <code>null</code> the default 
     564   * index of 0 will be used. 
     565   */ 
    566566  Boolean isDisplayRGB(Integer image); 
    567567 
    568568  /** 
    569569   * Gets the color map associated with the given pixels. 
    570    * @param image the index of the image.  If <code>null</code> the default  
    571    * index of 0 will be used. 
    572    */  
     570   * @param image the index of the image.  If <code>null</code> the default 
     571   * index of 0 will be used. 
     572   */ 
    573573  String getColorMap(Integer image); 
    574   
     574 
    575575  /** 
    576576   * Gets the minimum Z coordinate for which the display settings apply. 
    577    * @param image the index of the image.  If <code>null</code> the default  
    578    * index of 0 will be used. 
    579    */  
     577   * @param image the index of the image.  If <code>null</code> the default 
     578   * index of 0 will be used. 
     579   */ 
    580580  Integer getZStart(Integer image); 
    581581 
    582582  /** 
    583583   * Gets the maximum Z coordinate for which the display settings apply. 
    584    * @param image the index of the image.  If <code>null</code> the default  
    585    * index of 0 will be used. 
    586    */  
     584   * @param image the index of the image.  If <code>null</code> the default 
     585   * index of 0 will be used. 
     586   */ 
    587587  Integer getZStop(Integer image); 
    588588 
    589589  /** 
    590590   * Gets the minimum T coordinate for which the display settings apply. 
    591    * @param image the index of the image.  If <code>null</code> the default  
    592    * index of 0 will be used. 
    593    */  
     591   * @param image the index of the image.  If <code>null</code> the default 
     592   * index of 0 will be used. 
     593   */ 
    594594  Integer getTStart(Integer image); 
    595595 
    596596  /** 
    597597   * Gets the maximum T coordinate for which the display settings apply. 
    598    * @param image the index of the image.  If <code>null</code> the default  
    599    * index of 0 will be used. 
    600    */  
     598   * @param image the index of the image.  If <code>null</code> the default 
     599   * index of 0 will be used. 
     600   */ 
    601601  Integer getTStop(Integer image); 
    602602 
     
    605605  /** 
    606606   * Gets the manufacturer of the given light source. 
    607    * @param light the index of the light.  If <code>null</code> the default  
    608    * index of 0 will be used. 
    609    */  
     607   * @param light the index of the light.  If <code>null</code> the default 
     608   * index of 0 will be used. 
     609   */ 
    610610  String getLightManufacturer(Integer light); 
    611611 
    612612  /** 
    613613   * Gets the model of the given light source. 
    614    * @param light the index of the light.  If <code>null</code> the default  
    615    * index of 0 will be used. 
    616    */  
     614   * @param light the index of the light.  If <code>null</code> the default 
     615   * index of 0 will be used. 
     616   */ 
    617617  String getLightModel(Integer light); 
    618618 
    619619  /** 
    620620   * Gets the serial number of the given light source. 
    621    * @param light the index of the light.  If <code>null</code> the default  
    622    * index of 0 will be used. 
    623    */  
     621   * @param light the index of the light.  If <code>null</code> the default 
     622   * index of 0 will be used. 
     623   */ 
    624624  String getLightSerial(Integer light); 
    625625 
     
    630630   * @param laser the index of the laser.  If <code>null</code> the default 
    631631   * index of 0 will be used. 
    632    */  
     632   */ 
    633633  String getLaserType(Integer laser); 
    634634 
     
    637637   * @param laser the index of the laser.  If <code>null</code> the default 
    638638   * index of 0 will be used. 
    639    */  
     639   */ 
    640640  String getLaserMedium(Integer laser); 
    641641 
     
    644644   * @param laser the index of the laser.  If <code>null</code> the default 
    645645   * index of 0 will be used. 
    646    */  
     646   */ 
    647647  Integer getLaserWavelength(Integer laser); 
    648648 
     
    651651   * @param laser the index of the laser.  If <code>null</code> the default 
    652652   * index of 0 will be used. 
    653    */  
    654   Boolean isFrequencyDoubled(Integer laser);  
     653   */ 
     654  Boolean isFrequencyDoubled(Integer laser); 
    655655 
    656656  /** 
     
    658658   * @param laser the index of the laser.  If <code>null</code> the default 
    659659   * index of 0 will be used. 
    660    */  
     660   */ 
    661661  Boolean isTunable(Integer laser); 
    662662 
     
    665665   * @param laser the index of the laser.  If <code>null</code> the default 
    666666   * index of 0 will be used. 
    667    */  
     667   */ 
    668668  String getPulse(Integer laser); 
    669669 
     
    672672   * @param laser the index of the laser.  If <code>null</code> the default 
    673673   * index of 0 will be used. 
    674    */  
     674   */ 
    675675  Float getPower(Integer laser); 
    676676 
     
    679679  /** 
    680680   * Gets the type of the given filament. 
    681    * @param filament the index of the filament.  If <code>null</code> the  
    682    * default index of 0 will be used. 
    683    */  
     681   * @param filament the index of the filament.  If <code>null</code> the 
     682   * default index of 0 will be used. 
     683   */ 
    684684  String getFilamentType(Integer filament); 
    685685 
    686686  /** 
    687687   * Gets the power (in watts) of the given filament. 
    688    * @param filament the index of the filament.  If <code>null</code> the  
    689    * default index of 0 will be used. 
    690    */  
     688   * @param filament the index of the filament.  If <code>null</code> the 
     689   * default index of 0 will be used. 
     690   */ 
    691691  Float getFilamentPower(Integer filament); 
    692692 
     
    697697   * @param arc the index of the arc.  If <code>null</code> the default 
    698698   * index of 0 will be used. 
    699    */  
     699   */ 
    700700  String getArcType(Integer arc); 
    701701 
     
    704704   * @param arc the index of the arc.  If <code>null</code> the default 
    705705   * index of 0 will be used. 
    706    */  
     706   */ 
    707707  Float getArcPower(Integer arc); 
    708708 
     
    908908   * default index of 0 will be used. 
    909909   */ 
    910   Integer getOTFSizeX(Integer otf);  
     910  Integer getOTFSizeX(Integer otf); 
    911911 
    912912  /** 
     
    915915   * default index of 0 will be used. 
    916916   */ 
    917   Integer getOTFSizeY(Integer otf);  
     917  Integer getOTFSizeY(Integer otf); 
    918918 
    919919  /** 
  • trunk/loci/formats/MetadataStore.java

    r2426 r3015  
    3737 * {@link MetadataStoreException} if they are unable to initialize 
    3838 * some of their dependencies. 
     39 * 
     40 * <dl><dt><b>Source code:</b></dt> 
     41 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/MetadataStore.java">Trac</a>, 
     42 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/MetadataStore.java">SVN</a></dd></dl> 
    3943 * 
    4044 * @author Chris Allan callan at blackcat.ca 
  • trunk/loci/formats/MetadataStoreException.java

    r2178 r3015  
    2929 * is attempted and fails due to potentially missing prerequisites). 
    3030 * 
     31 * <dl><dt><b>Source code:</b></dt> 
     32 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/MetadataStoreException.java">Trac</a>, 
     33 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/MetadataStoreException.java">SVN</a></dd></dl> 
     34 * 
    3135 * @author Chris Allan callan at blackcat.ca 
    3236 */ 
  • trunk/loci/formats/MinMaxCalculator.java

    r2976 r3015  
    2929import java.util.*; 
    3030 
    31 /** Logic to compute minimum and maximum values for each channel. */ 
     31/** 
     32 * Logic to compute minimum and maximum values for each channel. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/MinMaxCalculator.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/MinMaxCalculator.java">SVN</a></dd></dl> 
     37 */ 
    3238public class MinMaxCalculator extends ReaderWrapper { 
    3339 
  • trunk/loci/formats/NumberFilter.java

    r2178 r3015  
    2929import java.math.BigInteger; 
    3030 
    31 /** NumberFilter is a helper filter for FilePattern.findPattern(). */ 
     31/** 
     32 * NumberFilter is a helper filter for FilePattern.findPattern(). 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/NumberFilter.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/NumberFilter.java">SVN</a></dd></dl> 
     37 */ 
    3238public class NumberFilter implements FileFilter { 
    3339 
  • trunk/loci/formats/RABytes.java

    r2455 r3015  
    2929/** 
    3030 * A wrapper for a byte array that implements the IRandomAccess interface. 
     31 * 
     32 * <dl><dt><b>Source code:</b></dt> 
     33 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/RABytes.java">Trac</a>, 
     34 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/RABytes.java">SVN</a></dd></dl> 
    3135 * 
    3236 * @see IRandomAccess 
  • trunk/loci/formats/RAFile.java

    r2455 r3015  
    2929/** 
    3030 * A wrapper for RandomAccessFile that implements the IRandomAccess interface. 
     31 * 
     32 * <dl><dt><b>Source code:</b></dt> 
     33 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/RAFile.java">Trac</a>, 
     34 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/RAFile.java">SVN</a></dd></dl> 
    3135 * 
    3236 * @see IRandomAccess 
  • trunk/loci/formats/RAUrl.java

    r2455 r3015  
    3131 * Provides random access to data over HTTP using the IRandomAccess interface. 
    3232 * This is slow, but functional. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/RAUrl.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/RAUrl.java">SVN</a></dd></dl> 
    3337 * 
    3438 * @see IRandomAccess 
  • trunk/loci/formats/RandomAccessStream.java

    r2976 r3015  
    3434 * byte arrays.  It also automagically deals with closing and reopening files 
    3535 * to prevent an IOException caused by too many open files. 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/RandomAccessStream.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/RandomAccessStream.java">SVN</a></dd></dl> 
    3640 * 
    3741 * @author Melissa Linkert, linkert at wisc.edu 
  • trunk/loci/formats/ReaderWrapper.java

    r2998 r3015  
    3232 * Abstract superclass of reader logic that wraps other readers. 
    3333 * All methods are simply delegated to the wrapped reader. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ReaderWrapper.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ReaderWrapper.java">SVN</a></dd></dl> 
    3438 */ 
    3539public abstract class ReaderWrapper implements IFormatReader { 
  • trunk/loci/formats/ReflectException.java

    r2178 r3015  
    2828 * ReflectException is the exception thrown when something 
    2929 * goes wrong performing a reflected operation with ReflectedUniverse. 
     30 * 
     31 * <dl><dt><b>Source code:</b></dt> 
     32 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ReflectException.java">Trac</a>, 
     33 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ReflectException.java">SVN</a></dd></dl> 
    3034 */ 
    3135public class ReflectException extends Exception { 
  • trunk/loci/formats/ReflectedUniverse.java

    r3011 r3015  
    2929import java.util.*; 
    3030 
    31 /** A general-purpose reflection wrapper class. */ 
     31/** 
     32 * A general-purpose reflection wrapper class. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ReflectedUniverse.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ReflectedUniverse.java">SVN</a></dd></dl> 
     37 */ 
    3238public class ReflectedUniverse { 
    3339 
  • trunk/loci/formats/StatusEvent.java

    r2453 r3015  
    2525package loci.formats; 
    2626 
    27 /** A event indicating a status update. */ 
     27/** 
     28 * A event indicating a status update. 
     29 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/StatusEvent.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/StatusEvent.java">SVN</a></dd></dl> 
     33 */ 
    2834public class StatusEvent { 
    2935 
  • trunk/loci/formats/StatusListener.java

    r2453 r3015  
    2525package loci.formats; 
    2626 
    27 /** A listener for status updates. */ 
     27/** 
     28 * A listener for status updates. 
     29 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/StatusListener.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/StatusListener.java">SVN</a></dd></dl> 
     33 */ 
    2834public interface StatusListener { 
    2935 
  • trunk/loci/formats/StatusReporter.java

    r2454 r3015  
    2525package loci.formats; 
    2626 
    27 /** Interface for components capable of reporting status updates. */ 
     27/** 
     28 * Interface for components capable of reporting status updates. 
     29 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/StatusReporter.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/StatusReporter.java">SVN</a></dd></dl> 
     33 */ 
    2834public interface StatusReporter { 
    2935 
  • trunk/loci/formats/TiffIFDEntry.java

    r2178 r3015  
    2929 * store the values from the entry's specific offset and is based on the TIFF 
    3030 * 6.0 specification of an IFD entry. 
     31 * 
     32 * <dl><dt><b>Source code:</b></dt> 
     33 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/TiffIFDEntry.java">Trac</a>, 
     34 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/TiffIFDEntry.java">SVN</a></dd></dl> 
    3135 * 
    3236 * @author Chris Allan callan at blackcat.ca 
  • trunk/loci/formats/TiffRational.java

    r2178 r3015  
    2525package loci.formats; 
    2626 
    27 /** A rational number (numerator over denominator). */ 
     27/** 
     28 * A rational number (numerator over denominator). 
     29 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/TiffRational.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/TiffRational.java">SVN</a></dd></dl> 
     33 */ 
    2834public class TiffRational extends Number implements Comparable { 
    2935 
  • trunk/loci/formats/TiffTools.java

    r2977 r3015  
    3636/** 
    3737 * A utility class for manipulating TIFF files. 
     38 * 
     39 * <dl><dt><b>Source code:</b></dt> 
     40 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/TiffTools.java">Trac</a>, 
     41 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/TiffTools.java">SVN</a></dd></dl> 
    3842 * 
    3943 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/UnknownTagException.java

    r2178 r3015  
    2828 * Thrown when a given entry does not have a particular tag. 
    2929 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/UnknownTagException.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/UnknownTagException.java">SVN</a></dd></dl> 
     33 * 
    3034 * @author Chris Allan callan at blackcat.ca 
    3135 */ 
  • trunk/loci/formats/cache/BufferedImageSource.java

    r3003 r3015  
    1111 * Retrieves BufferedImages from a data source 
    1212 * (e.g., a file) using Bio-Formats. 
     13 * 
     14 * <dl><dt><b>Source code:</b></dt> 
     15 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/BufferedImageSource.java">Trac</a>, 
     16 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/BufferedImageSource.java">SVN</a></dd></dl> 
    1317 */ 
    1418public class BufferedImageSource extends CacheSource { 
  • trunk/loci/formats/cache/ByteArraySource.java

    r3003 r3015  
    1111 * Retrieves byte arrays from a data source 
    1212 * (e.g., a file) using Bio-Formats. 
     13 * 
     14 * <dl><dt><b>Source code:</b></dt> 
     15 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/ByteArraySource.java">Trac</a>, 
     16 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/ByteArraySource.java">SVN</a></dd></dl> 
    1317 */ 
    1418public class ByteArraySource extends CacheSource { 
  • trunk/loci/formats/cache/Cache.java

    r3004 r3015  
    2121 * strategy indicating which surrounding planes to load into the cache (i.e., 
    2222 * planes within a certain range along each dimensional axis). 
     23 * 
     24 * <dl><dt><b>Source code:</b></dt> 
     25 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/Cache.java">Trac</a>, 
     26 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/Cache.java">SVN</a></dd></dl> 
    2327 */ 
    2428public class Cache implements CacheReporter { 
  • trunk/loci/formats/cache/CacheEvent.java

    r3003 r3015  
    2525package loci.formats.cache; 
    2626 
    27 /** A event indicating a cache update. */ 
     27/** 
     28 * A event indicating a cache update. 
     29 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/CacheEvent.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/CacheEvent.java">SVN</a></dd></dl> 
     33 */ 
    2834public class CacheEvent { 
    2935 
  • trunk/loci/formats/cache/CacheException.java

    r2961 r3015  
    1010 * CacheException is the exception thrown when something 
    1111 * goes wrong performing a cache operation. 
     12 * 
     13 * <dl><dt><b>Source code:</b></dt> 
     14 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/CacheException.java">Trac</a>, 
     15 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/CacheException.java">SVN</a></dd></dl> 
    1216 */ 
    1317public class CacheException extends FormatException { 
  • trunk/loci/formats/cache/CacheListener.java

    r3003 r3015  
    2525package loci.formats.cache; 
    2626 
    27 /** A listener for cache updates. */ 
     27/** 
     28 * A listener for cache updates. 
     29 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/CacheListener.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/CacheListener.java">SVN</a></dd></dl> 
     33 */ 
    2834public interface CacheListener { 
    2935 
  • trunk/loci/formats/cache/CacheReporter.java

    r3003 r3015  
    2525package loci.formats.cache; 
    2626 
    27 /** Interface for components capable of reporting cache updates. */ 
     27/** 
     28 * Interface for components capable of reporting cache updates. 
     29 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/CacheReporter.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/CacheReporter.java">SVN</a></dd></dl> 
     33 */ 
    2834public interface CacheReporter { 
    2935 
  • trunk/loci/formats/cache/CacheSource.java

    r3003 r3015  
    1111 * Superclass of cache sources that retrieve image planes 
    1212 * from a data source (e.g., a file) using Bio-Formats. 
     13 * 
     14 * <dl><dt><b>Source code:</b></dt> 
     15 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/CacheSource.java">Trac</a>, 
     16 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/CacheSource.java">SVN</a></dd></dl> 
    1317 */ 
    1418public abstract class CacheSource implements ICacheSource { 
  • trunk/loci/formats/cache/CacheStrategy.java

    r3003 r3015  
    88import loci.formats.FormatTools; 
    99 
    10 /** Superclass of cache strategies. */ 
     10/** 
     11 * Superclass of cache strategies. 
     12 * 
     13 * <dl><dt><b>Source code:</b></dt> 
     14 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/CacheStrategy.java">Trac</a>, 
     15 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/CacheStrategy.java">SVN</a></dd></dl> 
     16 */ 
    1117public abstract class CacheStrategy 
    1218  implements CacheReporter, Comparator, ICacheStrategy 
     
    278284 
    279285  // -- Helper methods -- 
    280    
     286 
    281287  /** Informs listeners of a cache update. */ 
    282288  protected void notifyListeners(CacheEvent e) { 
  • trunk/loci/formats/cache/CrosshairStrategy.java

    r3003 r3015  
    3131 *    4 |           5 
    3232 * </pre> 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/CrosshairStrategy.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/CrosshairStrategy.java">SVN</a></dd></dl> 
    3337 */ 
    3438public class CrosshairStrategy extends CacheStrategy { 
  • trunk/loci/formats/cache/ICacheSource.java

    r3003 r3015  
    1111 * Bio-Formats uses {@link loci.formats.IFormatReader} to obtain image planes, 
    1212 * but any ordered collection of objects can conceivably be cached. 
     13 * 
     14 * <dl><dt><b>Source code:</b></dt> 
     15 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/ICacheSource.java">Trac</a>, 
     16 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/ICacheSource.java">SVN</a></dd></dl> 
    1317 */ 
    1418public interface ICacheSource { 
  • trunk/loci/formats/cache/ICacheStrategy.java

    r3003 r3015  
    1111 * rather than rasterized (1-D) indices. The two are made equivalent via a 
    1212 * mapping between the two, invoked within {@link Cache} as needed. 
     13 * 
     14 * <dl><dt><b>Source code:</b></dt> 
     15 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/ICacheStrategy.java">Trac</a>, 
     16 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/ICacheStrategy.java">SVN</a></dd></dl> 
    1317 */ 
    1418public interface ICacheStrategy extends CacheReporter { 
  • trunk/loci/formats/cache/ImageProcessorSource.java

    r3003 r3015  
    1212 * Retrieves ImageJ image processors from a data source 
    1313 * (e.g., a file) using Bio-Formats. 
     14 * 
     15 * <dl><dt><b>Source code:</b></dt> 
     16 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/ImageProcessorSource.java">Trac</a>, 
     17 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/ImageProcessorSource.java">SVN</a></dd></dl> 
    1418 */ 
    1519public class ImageProcessorSource extends CacheSource { 
  • trunk/loci/formats/cache/RectangleStrategy.java

    r2976 r3015  
    3232 *    4 |    23 19  5 13 21 
    3333 * </pre> 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/cache/RectangleStrategy.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/cache/RectangleStrategy.java">SVN</a></dd></dl> 
    3438 */ 
    3539public class RectangleStrategy extends CacheStrategy { 
  • trunk/loci/formats/codec/AdobeDeflateCodec.java

    r2976 r3015  
    3333 * This class implements Adobe Deflate decompression. Compression is not yet 
    3434 * implemented. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/AdobeDeflateCodec.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/AdobeDeflateCodec.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/codec/BZip2Constants.java

    r2782 r3015  
    5050 * Base class for both the compress and decompress classes. 
    5151 * Holds common arrays, and static data. 
     52 * 
     53 * <dl><dt><b>Source code:</b></dt> 
     54 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/BZip2Constants.java">Trac</a>, 
     55 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/BZip2Constants.java">SVN</a></dd></dl> 
    5256 */ 
    5357public interface BZip2Constants { 
  • trunk/loci/formats/codec/Base64Codec.java

    r2976 r3015  
    3131 * for Base64.  This code was adapted from the Jakarta Commons Codec source, 
    3232 * http://jakarta.apache.org/commons 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/Base64Codec.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/Base64Codec.java">SVN</a></dd></dl> 
    3337 * 
    3438 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/codec/BaseCodec.java

    r2976 r3015  
    3636 * are left as abstract. 2D methods do simple concatenation and call to the 1D 
    3737 * methods 
     38 * 
     39 * <dl><dt><b>Source code:</b></dt> 
     40 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/BaseCodec.java">Trac</a>, 
     41 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/BaseCodec.java">SVN</a></dd></dl> 
    3842 * 
    3943 * @author Eric Kjellman egkjellman at wisc.edu 
  • trunk/loci/formats/codec/BitBuffer.java

    r2857 r3015  
    3030/** 
    3131 * A class for reading arbitrary numbers of bits from a byte array. 
     32 * <dl><dt><b>Source code:</b></dt> 
     33 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/BitBuffer.java">Trac</a>, 
     34 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/BitBuffer.java">SVN</a></dd></dl> 
     35 * 
    3236 * @author Eric Kjellman egkjellman at wisc.edu 
    3337 */ 
  • trunk/loci/formats/codec/BitWriter.java

    r2857 r3015  
    3030/** 
    3131 * A class for writing arbitrary numbers of bits to a byte array. 
     32 * <dl><dt><b>Source code:</b></dt> 
     33 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/BitWriter.java">Trac</a>, 
     34 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/BitWriter.java">SVN</a></dd></dl> 
     35 * 
    3236 * @author Curtis Rueden ctrueden at wisc.edu 
    3337 */ 
  • trunk/loci/formats/codec/ByteVector.java

    r2450 r3015  
    2727/** 
    2828 * A growable array of bytes. 
     29 * <dl><dt><b>Source code:</b></dt> 
     30 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/ByteVector.java">Trac</a>, 
     31 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/ByteVector.java">SVN</a></dd></dl> 
     32 * 
    2933 * @author Wayne Rasband wsr at nih.gov 
    3034 */ 
  • trunk/loci/formats/codec/CBZip2InputStream.java

    r2857 r3015  
    6868 * 
    6969 * <p>Instances of this class are not threadsafe.</p> 
     70 * 
     71 * <dl><dt><b>Source code:</b></dt> 
     72 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/CBZip2InputStream.java">Trac</a>, 
     73 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/CBZip2InputStream.java">SVN</a></dd></dl> 
    7074 */ 
    7175public class CBZip2InputStream extends InputStream implements BZip2Constants { 
  • trunk/loci/formats/codec/CRC.java

    r2782 r3015  
    5050 * A simple class the hold and calculate the CRC for sanity checking 
    5151 * of the data. 
     52 * 
     53 * <dl><dt><b>Source code:</b></dt> 
     54 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/CRC.java">Trac</a>, 
     55 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/CRC.java">SVN</a></dd></dl> 
    5256 */ 
    5357public class CRC { 
  • trunk/loci/formats/codec/Codec.java

    r2914 r3015  
    4141 * implement both compression methods or neither. (The same is expected for 
    4242 * decompression). 
     43 * 
     44 * <dl><dt><b>Source code:</b></dt> 
     45 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/Codec.java">Trac</a>, 
     46 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/Codec.java">SVN</a></dd></dl> 
    4347 * 
    4448 * @author Eric Kjellman egkjellman at wisc.edu 
  • trunk/loci/formats/codec/JPEGCodec.java

    r2976 r3015  
    3333 * This class implements JPEG decompression. Compression is not yet 
    3434 * implemented. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/JPEGCodec.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/JPEGCodec.java">SVN</a></dd></dl> 
    3539 */ 
    3640public class JPEGCodec extends BaseCodec implements Codec { 
  • trunk/loci/formats/codec/LZOCodec.java

    r2914 r3015  
    3030 * This class implements LZO decompression. Compression is not yet 
    3131 * implemented. 
     32 * 
     33 * <dl><dt><b>Source code:</b></dt> 
     34 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/LZOCodec.java">Trac</a>, 
     35 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/LZOCodec.java">SVN</a></dd></dl> 
    3236 * 
    3337 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/codec/LZWCodec.java

    r2914 r3015  
    3131 * TIFF 6.0 Specification at 
    3232 * http://partners.adobe.com/asn/developer/pdfs/tn/TIFF6.pdf (page 61). 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/LZWCodec.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/LZWCodec.java">SVN</a></dd></dl> 
    3337 * 
    3438 * @author Eric Kjellman egkjellman at wisc.edu 
  • trunk/loci/formats/codec/LZWTreeNode.java

    r2450 r3015  
    2727/** 
    2828 * An LZW-compression helper class for building a symbol table in tree format. 
     29 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/LZWTreeNode.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/LZWTreeNode.java">SVN</a></dd></dl> 
    2933 * 
    3034 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/codec/LuraWaveCodec.java

    r2914 r3015  
    3333 * license code, specified in the lurawave.license system property (e.g., 
    3434 * <code>-Dlurawave.license=XXXX</code> on the command line). 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/LuraWaveCodec.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/LuraWaveCodec.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/codec/MJPBCodec.java

    r2976 r3015  
    88import loci.formats.*; 
    99 
    10 /** Methods for compressing and decompressing QuickTime Motion JPEG-B data. */ 
     10/** 
     11 * Methods for compressing and decompressing QuickTime Motion JPEG-B data. 
     12 * 
     13 * <dl><dt><b>Source code:</b></dt> 
     14 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/MJPBCodec.java">Trac</a>, 
     15 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/MJPBCodec.java">SVN</a></dd></dl> 
     16 */ 
    1117public class MJPBCodec extends BaseCodec implements Codec { 
    1218 
  • trunk/loci/formats/codec/MSRLECodec.java

    r2976 r3015  
    77import loci.formats.*; 
    88 
    9 /** Methods for compressing and decompressing data using Microsoft RLE. */ 
     9/** 
     10 * Methods for compressing and decompressing data using Microsoft RLE. 
     11 * 
     12 * <dl><dt><b>Source code:</b></dt> 
     13 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/MSRLECodec.java">Trac</a>, 
     14 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/MSRLECodec.java">SVN</a></dd></dl> 
     15 */ 
    1016public class MSRLECodec extends BaseCodec implements Codec { 
    1117 
  • trunk/loci/formats/codec/NikonCodec.java

    r2914 r3015  
    3030 * This class implements Nikon decompression. Compression is not yet 
    3131 * implemented. 
     32 * 
     33 * <dl><dt><b>Source code:</b></dt> 
     34 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/NikonCodec.java">Trac</a>, 
     35 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/NikonCodec.java">SVN</a></dd></dl> 
    3236 * 
    3337 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/codec/PackbitsCodec.java

    r2914 r3015  
    3030 * This class implements packbits decompression. Compression is not yet 
    3131 * implemented. 
     32 * 
     33 * <dl><dt><b>Source code:</b></dt> 
     34 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/PackbitsCodec.java">Trac</a>, 
     35 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/PackbitsCodec.java">SVN</a></dd></dl> 
    3236 * 
    3337 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/codec/QTRLECodec.java

    r2976 r3015  
    88import loci.formats.*; 
    99 
    10 /** Methods for compressing and decompressing data using QuickTime RLE. */ 
     10/** 
     11 * Methods for compressing and decompressing data using QuickTime RLE. 
     12 * 
     13 * <dl><dt><b>Source code:</b></dt> 
     14 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/QTRLECodec.java">Trac</a>, 
     15 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/QTRLECodec.java">SVN</a></dd></dl> 
     16 */ 
    1117public class QTRLECodec extends BaseCodec implements Codec { 
    1218 
  • trunk/loci/formats/codec/RPZACodec.java

    r2976 r3015  
    3030 * Implements encoding and decoding methods for Apple RPZA.  This code was 
    3131 * adapted from the RPZA codec for ffmpeg - see http://ffmpeg.mplayerhq.hu 
     32 * 
     33 * <dl><dt><b>Source code:</b></dt> 
     34 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/codec/RPZACodec.java">Trac</a>, 
     35 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/codec/RPZACodec.java">SVN</a></dd></dl> 
    3236 */ 
    3337public class RPZACodec extends BaseCodec implements Codec { 
  • trunk/loci/formats/gui/CacheComponent.java

    r3008 r3015  
    1414import java.lang.reflect.Constructor; 
    1515 
    16 /** GUI component for managing a cache. */ 
     16/** 
     17 * GUI component for managing a cache. 
     18 * 
     19 * <dl><dt><b>Source code:</b></dt> 
     20 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/gui/CacheComponent.java">Trac</a>, 
     21 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/gui/CacheComponent.java">SVN</a></dd></dl> 
     22 */ 
    1723public class CacheComponent extends JPanel 
    1824  implements ActionListener, CacheListener, ChangeListener 
     
    4955    ICacheStrategy.BACKWARD_ORDER 
    5056  }; 
    51  
    5257 
    5358  // -- Fields -- 
  • trunk/loci/formats/gui/ComboFileFilter.java

    r2571 r3015  
    2929import javax.swing.filechooser.FileFilter; 
    3030 
    31 /** A file filter that recognizes files from a union of other filters. */ 
     31/** 
     32 * A file filter that recognizes files from a union of other filters. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/gui/ComboFileFilter.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/gui/ComboFileFilter.java">SVN</a></dd></dl> 
     37 */ 
    3238public class ComboFileFilter extends FileFilter 
    3339  implements java.io.FileFilter, Comparable 
  • trunk/loci/formats/gui/DataConverter.java

    r2954 r3015  
    4444 * A utility for reorganizing and converting QuickTime movies, 
    4545 * TIFF series and other 4D datasets. 
     46 * 
     47 * <dl><dt><b>Source code:</b></dt> 
     48 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/gui/DataConverter.java">Trac</a>, 
     49 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/gui/DataConverter.java">SVN</a></dd></dl> 
    4650 */ 
    4751public class DataConverter extends JFrame implements 
  • trunk/loci/formats/gui/ExtensionFileFilter.java

    r2538 r3015  
    2828import javax.swing.filechooser.FileFilter; 
    2929 
    30 /** A file filter based on file extensions, for use with a JFileChooser. */ 
     30/** 
     31 * A file filter based on file extensions, for use with a JFileChooser. 
     32 * 
     33 * <dl><dt><b>Source code:</b></dt> 
     34 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/gui/ExtensionFileFilter.java">Trac</a>, 
     35 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/gui/ExtensionFileFilter.java">SVN</a></dd></dl> 
     36 */ 
    3137public class ExtensionFileFilter extends FileFilter 
    3238  implements java.io.FileFilter, Comparable 
  • trunk/loci/formats/gui/FormatFileFilter.java

    r2571 r3015  
    2929import loci.formats.IFormatReader; 
    3030 
    31 /** A file filter for a biological file format, for use with a JFileChooser. */ 
     31/** 
     32 * A file filter for a biological file format, for use with a JFileChooser. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/gui/FormatFileFilter.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/gui/FormatFileFilter.java">SVN</a></dd></dl> 
     37 */ 
    3238public class FormatFileFilter extends FileFilter 
    3339  implements java.io.FileFilter, Comparable 
  • trunk/loci/formats/gui/GUITools.java

    r2881 r3015  
    3434/** 
    3535 * A utility class for working with graphical user interfaces. 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/gui/GUITools.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/gui/GUITools.java">SVN</a></dd></dl> 
    3640 * 
    3741 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/gui/ImageViewer.java

    r2979 r3015  
    3939 * ImageViewer is a simple viewer/converter 
    4040 * for the Bio-Formats image formats. 
     41 * 
     42 * <dl><dt><b>Source code:</b></dt> 
     43 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/gui/ImageViewer.java">Trac</a>, 
     44 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/gui/ImageViewer.java">SVN</a></dd></dl> 
    4145 * 
    4246 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/gui/PreviewPane.java

    r2954 r3015  
    4040 * PreviewPane is a panel for use as a JFileChooser accessory, displaying 
    4141 * a thumbnail for the selected image, loaded in a separate thread. 
     42 * 
     43 * <dl><dt><b>Source code:</b></dt> 
     44 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/gui/PreviewPane.java">Trac</a>, 
     45 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/gui/PreviewPane.java">SVN</a></dd></dl> 
    4246 */ 
    4347public class PreviewPane extends JPanel 
  • trunk/loci/formats/in/AVIReader.java

    r2994 r3015  
    3737 * Much of this form's code was adapted from Wayne Rasband's AVI Movie Reader 
    3838 * plugin for ImageJ (available at http://rsb.info.nih.gov/ij). 
     39 * 
     40 * <dl><dt><b>Source code:</b></dt> 
     41 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/AVIReader.java">Trac</a>, 
     42 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/AVIReader.java">SVN</a></dd></dl> 
    3943 */ 
    4044public class AVIReader extends FormatReader { 
     
    105109    } 
    106110 
    107     byte[] buf =  
     111    byte[] buf = 
    108112      new byte[core.sizeY[0] * effectiveWidth * bytes * core.sizeC[0]]; 
    109113    return openBytes(no, buf); 
     
    161165 
    162166      byte[] b = new byte[rawSize]; 
    163       
     167 
    164168      int len = rawSize / core.sizeY[0]; 
    165169      for (int y=0; y<core.sizeY[0]; y++) { 
    166         in.read(b, (core.sizeY[0] - y - 1) * len, len);  
    167       } 
    168        
     170        in.read(b, (core.sizeY[0] - y - 1) * len, len); 
     171      } 
     172 
    169173      BitBuffer bb = new BitBuffer(b); 
    170174 
    171175      for (int i=0; i<buf.length; i++) { 
    172176        buf[i] = (byte) bb.getBits(bmpBitsPerPixel); 
    173       }  
     177      } 
    174178 
    175179      return buf; 
     
    181185    for (int i=core.sizeY[0] - 1; i>=0; i--) { 
    182186      in.read(buf, i*scanline, scanline); 
    183       if (bmpBitsPerPixel == 24) {  
     187      if (bmpBitsPerPixel == 24) { 
    184188        for (int j=0; j<core.sizeX[0]; j++) { 
    185189          byte r = buf[i*scanline + j*3 + 2]; 
     
    190194      in.skipBytes(pad * (bmpBitsPerPixel / 8)); 
    191195    } 
    192      
     196 
    193197    if (bmpBitsPerPixel == 16) { 
    194198      // channels are separated, need to swap them 
     
    198202      System.arraycopy(r, 0, buf, 0, r.length); 
    199203    } 
    200      
     204 
    201205    return buf; 
    202206  } 
     
    206210    FormatTools.assertId(currentId, true, 1); 
    207211    return ImageTools.makeImage(openBytes(no), 
    208       core.sizeX[0], core.sizeY[0], core.sizeC[0], !core.interleaved[0],  
     212      core.sizeX[0], core.sizeY[0], core.sizeC[0], !core.interleaved[0], 
    209213      FormatTools.getBytesPerPixel(core.pixelType[0]), core.littleEndian[0]); 
    210214  } 
     
    247251      if (listString.equals(" JUN")) { 
    248252        in.skipBytes(1); 
    249         pos++;  
     253        pos++; 
    250254      } 
    251255 
     
    385389                } 
    386390 
    387                 if (!(bmpBitsPerPixel == 4 || bmpBitsPerPixel == 8 ||  
    388                   bmpBitsPerPixel == 24 || bmpBitsPerPixel == 16 ||  
     391                if (!(bmpBitsPerPixel == 4 || bmpBitsPerPixel == 8 || 
     392                  bmpBitsPerPixel == 24 || bmpBitsPerPixel == 16 || 
    389393                  bmpBitsPerPixel == 32)) 
    390394                { 
  • trunk/loci/formats/in/AliconaReader.java

    r2922 r3015  
    3030import loci.formats.*; 
    3131 
    32 /** AliconaReader is the file format reader for Alicona AL3D files. */ 
     32/** 
     33 * AliconaReader is the file format reader for Alicona AL3D files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/AliconaReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/AliconaReader.java">SVN</a></dd></dl> 
     38 */ 
    3339public class AliconaReader extends FormatReader { 
    3440 
  • trunk/loci/formats/in/BMPReader.java

    r2976 r3015  
    3333 * See http://astronomy.swin.edu.au/~pbourke/dataformats/bmp/ for a nice 
    3434 * description of the BMP file format. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/BMPReader.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/BMPReader.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/BaseTiffReader.java

    r2922 r3015  
    3636 * BaseTiffReader is the superclass for file format readers compatible with 
    3737 * or derived from the TIFF 6.0 file format. 
     38 * 
     39 * <dl><dt><b>Source code:</b></dt> 
     40 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/BaseTiffReader.java">Trac</a>, 
     41 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/BaseTiffReader.java">SVN</a></dd></dl> 
    3842 * 
    3943 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/in/BioRadReader.java

    r2999 r3015  
    3333/** 
    3434 * BioRadReader is the file format reader for Bio-Rad PIC files. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/BioRadReader.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/BioRadReader.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/in/DeltavisionReader.java

    r2999 r3015  
    3131/** 
    3232 * DeltavisionReader is the file format reader for Deltavision files. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/DeltavisionReader.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/DeltavisionReader.java">SVN</a></dd></dl> 
    3337 * 
    3438 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/DicomReader.java

    r2999 r3015  
    3535 * Much of this code is adapted from ImageJ's DICOM reader; see 
    3636 * http://rsb.info.nih.gov/ij/developer/source/ij/plugin/DICOM.java.html 
     37 * 
     38 * <dl><dt><b>Source code:</b></dt> 
     39 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/DicomReader.java">Trac</a>, 
     40 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/DicomReader.java">SVN</a></dd></dl> 
    3741 */ 
    3842public class DicomReader extends FormatReader { 
  • trunk/loci/formats/in/EPSReader.java

    r2976 r3015  
    3434 * Reader is the file format reader for Encapsulated PostScript (EPS) files. 
    3535 * Some regular PostScript files are also supported. 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/EPSReader.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/EPSReader.java">SVN</a></dd></dl> 
    3640 * 
    3741 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/FitsReader.java

    r2976 r3015  
    3434 * 
    3535 * Much of this code was adapted from ImageJ (http://rsb.info.nih.gov/ij). 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/FitsReader.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/FitsReader.java">SVN</a></dd></dl> 
    3640 */ 
    3741public class FitsReader extends FormatReader { 
  • trunk/loci/formats/in/FlexReader.java

    r2857 r3015  
    4141 * and a LuraWave license key must be specified in the lurawave.license system 
    4242 * property (e.g., <code>-Dlurawave.license=XXXX</code> on the command line). 
     43 * 
     44 * <dl><dt><b>Source code:</b></dt> 
     45 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/FlexReader.java">Trac</a>, 
     46 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/FlexReader.java">SVN</a></dd></dl> 
    4347 */ 
    4448public class FlexReader extends BaseTiffReader { 
  • trunk/loci/formats/in/FluoviewReader.java

    r2976 r3015  
    3333 * FluoviewReader is the file format reader for 
    3434 * Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/FluoviewReader.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/FluoviewReader.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Eric Kjellman egkjellman at wisc.edu 
  • trunk/loci/formats/in/GIFReader.java

    r2976 r3015  
    3434 * (GIF) files.  Much of this code was adapted from the Animated GIF Reader 
    3535 * plugin for ImageJ (http://rsb.info.nih.gov/ij). 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/GIFReader.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/GIFReader.java">SVN</a></dd></dl> 
    3640 */ 
    3741public class GIFReader extends FormatReader { 
  • trunk/loci/formats/in/GatanReader.java

    r2976 r3015  
    3232/** 
    3333 * GatanReader is the file format reader for Gatan files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/GatanReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/GatanReader.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/GelReader.java

    r2857 r3015  
    3131 * GelReader is the file format reader for 
    3232 * Molecular Dynamics GEL TIFF files. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/GelReader.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/GelReader.java">SVN</a></dd></dl> 
    3337 * 
    3438 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/ICSReader.java

    r2970 r3015  
    3535 * ICSReader is the file format reader for ICS (Image Cytometry Standard) 
    3636 * files. More information on ICS can be found at http://libics.sourceforge.net 
     37 * 
     38 * <dl><dt><b>Source code:</b></dt> 
     39 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/ICSReader.java">Trac</a>, 
     40 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/ICSReader.java">SVN</a></dd></dl> 
    3741 * 
    3842 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/IPLabReader.java

    r2976 r3015  
    3131/** 
    3232 * IPLabReader is the file format reader for IPLab (.IPL) files. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/IPLabReader.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/IPLabReader.java">SVN</a></dd></dl> 
    3337 * 
    3438 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/IPWReader.java

    r2976 r3015  
    3232/** 
    3333 * IPWReader is the file format reader for Image-Pro Workspace (IPW) files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/IPWReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/IPWReader.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/ImageIOReader.java

    r2701 r3015  
    3535 * ImageIOReader is the superclass for file format readers 
    3636 * that use the javax.imageio package. 
     37 * 
     38 * <dl><dt><b>Source code:</b></dt> 
     39 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/ImageIOReader.java">Trac</a>, 
     40 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/ImageIOReader.java">SVN</a></dd></dl> 
    3741 * 
    3842 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/in/ImarisReader.java

    r2976 r3015  
    3333 * Specifications available at 
    3434 * http://flash.bitplane.com/support/faqs/faqsview.cfm?inCat=6&inQuestionID=104 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/ImarisReader.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/ImarisReader.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/ImarisTiffReader.java

    r2922 r3015  
    3232 * ImarisTiffReader is the file format reader for 
    3333 * Imaris 5 files (TIFF variant). 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/ImarisTiffReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/ImarisTiffReader.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/ImprovisionTiffReader.java

    r2995 r3015  
    3232 * ImprovisionTiffReader is the file format reader for 
    3333 * Improvision TIFF files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/ImprovisionTiffReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/ImprovisionTiffReader.java">SVN</a></dd></dl> 
    3438 */ 
    3539public class ImprovisionTiffReader extends BaseTiffReader { 
     
    9599    String tc = (String) getMeta("TotalChannels"); 
    96100    String tt = (String) getMeta("TotalTimepoints"); 
    97      
     101 
    98102    if (tz == null) tz = "1"; 
    99103    if (tc == null) tc = "1"; 
  • trunk/loci/formats/in/JPEGReader.java

    r2557 r3015  
    2828 * JPEGReader is the file format reader for JPEG images. 
    2929 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/JPEGReader.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/JPEGReader.java">SVN</a></dd></dl> 
     33 * 
    3034 * @author Curtis Rueden ctrueden at wisc.edu 
    3135 */ 
  • trunk/loci/formats/in/KhorosReader.java

    r2976 r3015  
    2929import loci.formats.*; 
    3030 
    31 /** Reader for Khoros XV files. */ 
     31/** 
     32 * Reader for Khoros XV files. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/KhorosReader.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/KhorosReader.java">SVN</a></dd></dl> 
     37 */ 
    3238public class KhorosReader extends FormatReader { 
    3339 
  • trunk/loci/formats/in/LIFReader.java

    r3009 r3015  
    3636/** 
    3737 * LIFReader is the file format reader for Leica LIF files. 
     38 * 
     39 * <dl><dt><b>Source code:</b></dt> 
     40 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/LIFReader.java">Trac</a>, 
     41 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/LIFReader.java">SVN</a></dd></dl> 
    3842 * 
    3943 * @author Melissa Linkert linkert at wisc.edu 
     
    178182 
    179183      int blockLength = in.readInt(); 
    180       if (in.read() != 0x2a) {  
     184      if (in.read() != 0x2a) { 
    181185        in.skipBytes(3); 
    182186        if (in.read() != 0x2a) { 
    183187          throw new FormatException("Invalid Memory Description"); 
    184         }  
     188        } 
    185189      } 
    186190 
     
    341345                idx = numDatasets - 1; 
    342346              } 
    343               prefix = (String) seriesNames.get(idx);  
     347              prefix = (String) seriesNames.get(idx); 
    344348            } 
    345349 
     
    535539          fullSeries = fullSeries.substring(0, fullSeries.lastIndexOf("/")); 
    536540        } 
    537         else fullSeries = "";  
    538       }  
    539     }  
     541        else fullSeries = ""; 
     542      } 
     543    } 
    540544 
    541545    public void startElement(String uri, String localName, String qName, 
     
    545549        if (!attributes.getValue("Name").equals("DCROISet") && !firstElement) { 
    546550          series = attributes.getValue("Name"); 
    547           containerNames.add(series);  
     551          containerNames.add(series); 
    548552          if (fullSeries == null || fullSeries.equals("")) fullSeries = series; 
    549553          else fullSeries += "/" + series; 
    550554        } 
    551         else if (firstElement) firstElement = false;  
    552          
     555        else if (firstElement) firstElement = false; 
     556 
    553557        if (attributes.getValue("Name").equals("DCROISet")) { 
    554558          dcroiOpen = true; 
     
    676680      } 
    677681      else if (qName.equals("Laser")) { 
    678         String prefix = fullSeries + " Laser " +  
     682        String prefix = fullSeries + " Laser " + 
    679683          attributes.getValue("LaserName") + " - "; 
    680684        addMeta(prefix + "CanDoLinearOutputPower", 
     
    699703        String n = String.valueOf(count); 
    700704        while (n.length() < 4) n = "0" + n; 
    701         addMeta(fullSeries + " - TimeStamp " + n,  
     705        addMeta(fullSeries + " - TimeStamp " + n, 
    702706          DataTools.convertDate(ms, DataTools.COBOL)); 
    703707        count++; 
  • trunk/loci/formats/in/LegacyPictReader.java

    r2922 r3015  
    3232 * LegacyPictReader is the old file format reader for Apple PICT files. 
    3333 * To use it, QuickTime for Java must be installed. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/LegacyPictReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/LegacyPictReader.java">SVN</a></dd></dl> 
    3438 */ 
    3539public class LegacyPictReader extends FormatReader { 
  • trunk/loci/formats/in/LegacyQTReader.java

    r2701 r3015  
    3939 * Much of this code was based on the QuickTime Movie Opener for ImageJ 
    4040 * (available at http://rsb.info.nih.gov/ij/plugins/movie-opener.html). 
     41 * 
     42 * <dl><dt><b>Source code:</b></dt> 
     43 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/LegacyQTReader.java">Trac</a>, 
     44 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/LegacyQTReader.java">SVN</a></dd></dl> 
    4145 */ 
    4246public class LegacyQTReader extends FormatReader { 
  • trunk/loci/formats/in/LegacyZVIReader.java

    r2976 r3015  
    3434/** 
    3535 * LegacyZVIReader is the legacy file format reader for Zeiss ZVI files. 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/LegacyZVIReader.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/LegacyZVIReader.java">SVN</a></dd></dl> 
    3640 * 
    3741 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/in/LeicaReader.java

    r2999 r3015  
    3333/** 
    3434 * LeicaReader is the file format reader for Leica files. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/LeicaReader.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/LeicaReader.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/MDBParser.java

    r2857 r3015  
    2828import loci.formats.*; 
    2929 
    30 /** Utility class for parsing MDB database files. */ 
     30/** 
     31 * Utility class for parsing MDB database files. 
     32 * 
     33 * <dl><dt><b>Source code:</b></dt> 
     34 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/MDBParser.java">Trac</a>, 
     35 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/MDBParser.java">SVN</a></dd></dl> 
     36 */ 
    3137public final class MDBParser { 
    3238 
  • trunk/loci/formats/in/MNGReader.java

    r2922 r3015  
    3434 * MNGReader is the file format reader for Multiple Network Graphics (MNG) 
    3535 * files.  Does not support JNG (JPEG Network Graphics). 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/MNGReader.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/MNGReader.java">SVN</a></dd></dl> 
    3640 */ 
    3741public class MNGReader extends FormatReader { 
  • trunk/loci/formats/in/MRCReader.java

    r2976 r3015  
    3333 * Specifications available at 
    3434 * http://bio3d.colorado.edu/imod/doc/mrc_format.txt 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/MRCReader.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/MRCReader.java">SVN</a></dd></dl> 
    3539 */ 
    3640public class MRCReader extends FormatReader { 
  • trunk/loci/formats/in/MetamorphReader.java

    r2999 r3015  
    3333/** 
    3434 * Reader is the file format reader for Metamorph STK files. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/MetamorphReader.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/MetamorphReader.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Eric Kjellman egkjellman at wisc.edu 
  • trunk/loci/formats/in/MicromanagerReader.java

    r2996 r3015  
    3030import loci.formats.*; 
    3131 
    32 /** MicromanagerReader is the file format reader for Micro-Manager files. */ 
     32/** 
     33 * MicromanagerReader is the file format reader for Micro-Manager files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/MicromanagerReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/MicromanagerReader.java">SVN</a></dd></dl> 
     38 */ 
    3339public class MicromanagerReader extends FormatReader { 
    3440 
     
    106112    Location parent = new Location(name).getAbsoluteFile().getParentFile(); 
    107113    String[] list = parent.list(); 
    108     if (list == null) return false;  
     114    if (list == null) return false; 
    109115    for (int i=0; i<list.length; i++) { 
    110116      if (list[i].endsWith("metadata.txt")) return super.isThisType(name, open); 
  • trunk/loci/formats/in/ND2Reader.java

    r3011 r3015  
    4444 * (1) the JJ2000 jar file is *not* in the classpath; or 
    4545 * (2) the JAI jar file precedes JJ2000 in the classpath. 
     46 * 
     47 * <dl><dt><b>Source code:</b></dt> 
     48 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/ND2Reader.java">Trac</a>, 
     49 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/ND2Reader.java">SVN</a></dd></dl> 
    4650 */ 
    4751public class ND2Reader extends FormatReader { 
  • trunk/loci/formats/in/NRRDReader.java

    r2976 r3015  
    3030import loci.formats.*; 
    3131 
    32 /** File format reader for NRRD files;  see http://teem.sourceforge.net/nrrd. */ 
     32/** 
     33 * File format reader for NRRD files;  see http://teem.sourceforge.net/nrrd. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/NRRDReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/NRRDReader.java">SVN</a></dd></dl> 
     38 */ 
    3339public class NRRDReader extends FormatReader { 
    3440 
  • trunk/loci/formats/in/NikonReader.java

    r2857 r3015  
    3232 * NikonReader is the file format reader for 
    3333 * Nikon NEF (TIFF) files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/NikonReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/NikonReader.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/OIBReader.java

    r2976 r3015  
    3333/** 
    3434 * OIBReader is the file format reader for Fluoview FV1000 OIB files. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/OIBReader.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/OIBReader.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/OIFReader.java

    r2976 r3015  
    3333/** 
    3434 * OIFReader is the file format reader for Fluoview FV 1000 OIF files. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/OIFReader.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/OIFReader.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/OMETiffReader.java

    r3007 r3015  
    3535 * OMETiffReader is the file format reader for OME-TIFF files. 
    3636 * See http://www.loci.wisc.edu/ome/ome-tiff-spec.html 
     37 * 
     38 * <dl><dt><b>Source code:</b></dt> 
     39 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/OMETiffReader.java">Trac</a>, 
     40 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/OMETiffReader.java">SVN</a></dd></dl> 
    3741 */ 
    3842public class OMETiffReader extends BaseTiffReader { 
     
    136140        int sc = core.sizeC[i]; 
    137141        if (rgb) sc /= 3; 
    138         core.rgb[i] = rgb;  
     142        core.rgb[i] = rgb; 
    139143        core.sizeT[i] = Integer.parseInt(pixels[i].getAttribute("SizeT")); 
    140144        core.pixelType[i] = FormatTools.pixelTypeFromString( 
  • trunk/loci/formats/in/OMEXMLReader.java

    r2922 r3015  
    3535/** 
    3636 * OMEXMLReader is the file format reader for OME-XML files. 
     37 * 
     38 * <dl><dt><b>Source code:</b></dt> 
     39 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/OMEXMLReader.java">Trac</a>, 
     40 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/OMEXMLReader.java">SVN</a></dd></dl> 
    3741 * 
    3842 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/OpenlabRawReader.java

    r2976 r3015  
    3636 * Specifications available at 
    3737 * http://www.improvision.com/support/tech_notes/detail.php?id=344 
     38 * 
     39 * <dl><dt><b>Source code:</b></dt> 
     40 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/OpenlabRawReader.java">Trac</a>, 
     41 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/OpenlabRawReader.java">SVN</a></dd></dl> 
    3842 * 
    3943 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/OpenlabReader.java

    r2976 r3015  
    3434/** 
    3535 * OpenlabReader is the file format reader for Openlab LIFF files. 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/OpenlabReader.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/OpenlabReader.java">SVN</a></dd></dl> 
    3640 * 
    3741 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/PGMReader.java

    r2976 r3015  
    3434 * 
    3535 * Much of this code was adapted from ImageJ (http://rsb.info.nih.gov/ij). 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/PGMReader.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/PGMReader.java">SVN</a></dd></dl> 
    3640 */ 
    3741public class PGMReader extends FormatReader { 
  • trunk/loci/formats/in/PNGReader.java

    r2976 r3015  
    2929 * Portable Network Graphics (PNG) images. 
    3030 * 
     31 * <dl><dt><b>Source code:</b></dt> 
     32 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/PNGReader.java">Trac</a>, 
     33 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/PNGReader.java">SVN</a></dd></dl> 
     34 * 
    3135 * @author Curtis Rueden ctrueden at wisc.edu 
    3236 */ 
  • trunk/loci/formats/in/PerkinElmerReader.java

    r2976 r3015  
    3434/** 
    3535 * PerkinElmerReader is the file format reader for PerkinElmer files. 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/PerkinElmerReader.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/PerkinElmerReader.java">SVN</a></dd></dl> 
    3640 * 
    3741 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/PictReader.java

    r2976 r3015  
    3737 * (http://java.sun.com/products/jimi/index.html), ImageMagick 
    3838 * (http://www.imagemagick.org), and Java QuickDraw. 
     39 * 
     40 * <dl><dt><b>Source code:</b></dt> 
     41 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/PictReader.java">Trac</a>, 
     42 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/PictReader.java">SVN</a></dd></dl> 
    3943 */ 
    4044public class PictReader extends FormatReader { 
  • trunk/loci/formats/in/PrairieReader.java

    r2800 r3015  
    3434 * PrairieReader is the file format reader for 
    3535 * Prairie Technologies' TIFF variant. 
     36 * 
     37 * <dl><dt><b>Source code:</b></dt> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/PrairieReader.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/PrairieReader.java">SVN</a></dd></dl> 
    3640 */ 
    3741public class PrairieReader extends FormatReader { 
  • trunk/loci/formats/in/QTReader.java

    r2981 r3015  
    3838 * Video codecs currently supported: raw, rle, jpeg, mjpb, rpza. 
    3939 * Additional video codecs will be added as time permits. 
     40 * 
     41 * <dl><dt><b>Source code:</b></dt> 
     42 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/QTReader.java">Trac</a>, 
     43 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/QTReader.java">SVN</a></dd></dl> 
    4044 * 
    4145 * @author Melissa Linkert linkert at wisc.edu 
     
    157161    boolean doLegacy = useLegacy; 
    158162    if (!doLegacy && !code.equals("raw ") && !code.equals("rle ") && 
    159       !code.equals("jpeg") && !code.equals("mjpb") && !code.equals("rpza"))  
     163      !code.equals("jpeg") && !code.equals("mjpb") && !code.equals("rpza")) 
    160164    { 
    161165      if (debug) { 
     
    271275    boolean doLegacy = useLegacy; 
    272276    if (!doLegacy && !code.equals("raw ") && !code.equals("rle ") && 
    273       !code.equals("jpeg") && !code.equals("mjpb") && !code.equals("rpza"))  
     277      !code.equals("jpeg") && !code.equals("mjpb") && !code.equals("rpza")) 
    274278    { 
    275279      if (debug) { 
     
    596600          // found video codec and pixel depth information 
    597601 
    598           in.readInt();  
     602          in.readInt(); 
    599603          int numEntries = in.readInt(); 
    600           in.readInt();  
     604          in.readInt(); 
    601605 
    602606          for (int i=0; i<numEntries; i++) { 
     
    605609              in.skipBytes(16); 
    606610              if (in.readShort() == 0) { 
    607                 in.skipBytes(56);  
     611                in.skipBytes(56); 
    608612 
    609613                bitsPerPixel = in.readShort(); 
     
    617621                in.readDouble(); 
    618622                in.read(); 
    619               }  
     623              } 
    620624            } 
    621625            else { 
  • trunk/loci/formats/in/SDTInfo.java

    r2178 r3015  
    3232 * SDTInfo encapsulates the header information for 
    3333 * Becker &amp; Hickl SPC-Image SDT files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/SDTInfo.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/SDTInfo.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/in/SDTReader.java

    r2798 r3015  
    3232 * SDTReader is the file format reader for 
    3333 * Becker &amp; Hickl SPC-Image SDT files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/SDTReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/SDTReader.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/in/SEQReader.java

    r2673 r3015  
    3131/** 
    3232 * SEQReader is the file format reader for Image-Pro Sequence files. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/SEQReader.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/SEQReader.java">SVN</a></dd></dl> 
    3337 * 
    3438 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/SlidebookReader.java

    r2976 r3015  
    3535 * The strategies employed by this reader are highly suboptimal, as we 
    3636 * have very little information on the Slidebook format. 
     37 * 
     38 * <dl><dt><b>Source code:</b></dt> 
     39 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/SlidebookReader.java">Trac</a>, 
     40 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/SlidebookReader.java">SVN</a></dd></dl> 
    3741 * 
    3842 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/in/TCSReader.java

    r2976 r3015  
    3232/** 
    3333 * TCSReader is the file format reader for Leica TCS TIFF files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/TCSReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/TCSReader.java">SVN</a></dd></dl> 
    3438 */ 
    3539public class TCSReader extends BaseTiffReader { 
  • trunk/loci/formats/in/TiffReader.java

    r2999 r3015  
    3131/** 
    3232 * TiffReader is the file format reader for TIFF files, including OME-TIFF. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/TiffReader.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/TiffReader.java">SVN</a></dd></dl> 
    3337 * 
    3438 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/in/VisitechReader.java

    r2976 r3015  
    3030import loci.formats.*; 
    3131 
    32 /** VisitechReader is the file format reader for Visitech XYS files. */ 
     32/** 
     33 * VisitechReader is the file format reader for Visitech XYS files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/VisitechReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/VisitechReader.java">SVN</a></dd></dl> 
     38 */ 
    3339public class VisitechReader extends FormatReader { 
    3440 
  • trunk/loci/formats/in/ZeissLSMReader.java

    r2999 r3015  
    3232/** 
    3333 * ZeissLSMReader is the file format reader for Zeiss LSM files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/ZeissLSMReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/ZeissLSMReader.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Eric Kjellman egkjellman at wisc.edu 
  • trunk/loci/formats/in/ZeissZVIReader.java

    r3012 r3015  
    3232/** 
    3333 * ZeissZVIReader is the file format reader for Zeiss ZVI files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/ZeissZVIReader.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/ZeissZVIReader.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Melissa Linkert linkert at wisc.edu 
     
    392396      String emWave = (String) getMeta("Emission Wavelength " + idx); 
    393397      String exWave = (String) getMeta("Excitation Wavelength " + idx); 
    394       
     398 
    395399      if (emWave != null && emWave.indexOf(".") != -1) { 
    396400        emWave = emWave.substring(0, emWave.indexOf(".")); 
     
    400404      } 
    401405 
    402       store.setLogicalChannel(i, name, null,  
    403         emWave == null ? null : new Integer(emWave),  
     406      store.setLogicalChannel(i, name, null, 
     407        emWave == null ? null : new Integer(emWave), 
    404408        exWave == null ? null : new Integer(exWave), null, null, null); 
    405     
     409 
    406410      String black = (String) getMeta("BlackValue " + idx); 
    407411      String white = (String) getMeta("WhiteValue " + idx); 
    408412      String gamma = (String) getMeta("GammaValue " + idx); 
    409       
     413 
    410414      Double blackValue = null, whiteValue = null; 
    411415      Float gammaValue = null; 
     
    417421      try { gammaValue = new Float(gamma); } 
    418422      catch (Exception e) { } 
    419        
    420       store.setDisplayChannel(new Integer(i), blackValue, whiteValue,  
    421         gammaValue, null);  
    422     } 
    423    
     423 
     424      store.setDisplayChannel(new Integer(i), blackValue, whiteValue, 
     425        gammaValue, null); 
     426    } 
     427 
    424428    for (int i=0; i<core.imageCount[0]; i++) { 
    425429      int[] zct = FormatTools.getZCTCoords(this, i); 
    426430      String exposure = (String) getMeta("Exposure Time [ms] " + i); 
    427       store.setPlaneInfo(zct[0], zct[1], zct[2], null,  
     431      store.setPlaneInfo(zct[0], zct[1], zct[2], null, 
    428432      exposure == null ? null : new Float(exposure), null); 
    429433    } 
     
    442446    String objectiveNA = (String) getMeta("Objective N.A. 0"); 
    443447    if (objectiveNA != null) objectiveNA = DataTools.stripString(objectiveNA); 
    444     else objectiveNA = "1.0";  
     448    else objectiveNA = "1.0"; 
    445449 
    446450    store.setObjective(null, objectiveName, null, new Float(objectiveNA), 
     
    503507          dirName.toUpperCase().equals("ROOTENTRY")) 
    504508        { 
    505           if (entryName.equals("Tags")) parseTags(s);  
     509          if (entryName.equals("Tags")) parseTags(s); 
    506510        } 
    507511        else if (dirName.equals("Tags") && isContents) { 
     
    730734      String key = getKey(tagID); 
    731735      if (key.equals("Image Index Z")) { 
    732         try {  
    733           zIndex = Integer.parseInt(DataTools.stripString(value));  
     736        try { 
     737          zIndex = Integer.parseInt(DataTools.stripString(value)); 
    734738        } 
    735739        catch (NumberFormatException f) { } 
    736740      } 
    737741      else if (key.equals("Image Index T")) { 
    738         try {  
    739           tIndex = Integer.parseInt(DataTools.stripString(value));  
     742        try { 
     743          tIndex = Integer.parseInt(DataTools.stripString(value)); 
    740744        } 
    741745        catch (NumberFormatException f) { } 
    742746      } 
    743747      else if (key.equals("Image Channel Index")) { 
    744         try {  
    745           cIndex = Integer.parseInt(DataTools.stripString(value));  
     748        try { 
     749          cIndex = Integer.parseInt(DataTools.stripString(value)); 
    746750        } 
    747751        catch (NumberFormatException f) { } 
    748752      } 
    749753      else if (key.equals("ImageWidth")) { 
    750         try {  
     754        try { 
    751755          if (core.sizeX[0] == 0) core.sizeX[0] = Integer.parseInt(value); 
    752756        } 
     
    754758      } 
    755759      else if (key.equals("ImageHeight")) { 
    756         try {  
     760        try { 
    757761          if (core.sizeY[0] == 0) core.sizeY[0] = Integer.parseInt(value); 
    758762        } 
     
    764768          metadata.remove(key); 
    765769        } 
    766          
     770 
    767771        int ndx = 0; 
    768772        while (metadata.get(key + " " + ndx) != null) ndx++; 
    769         key += " " + ndx;  
    770       } 
    771        
     773        key += " " + ndx; 
     774      } 
     775 
    772776      addMeta(key, value); 
    773777 
     
    775779  } 
    776780 
    777   /** Return the string corresponding to the given ID. */  
     781  /** Return the string corresponding to the given ID. */ 
    778782  private String getKey(int tagID) { 
    779783    switch (tagID) { 
    780       case 222: return "Compression";  
     784      case 222: return "Compression"; 
    781785      case 258: return "BlackValue"; 
    782786      case 259: return "WhiteValue"; 
     
    11881192      case 101777411: 
    11891193        return "Image Name"; 
    1190       default: return "" + tagID;  
     1194      default: return "" + tagID; 
    11911195    } 
    11921196  } 
  • trunk/loci/formats/ome/OMEReader.java

    r2976 r3015  
    4343 * 
    4444 * where [server] is the URL of the OME data server (not the image server). 
     45 * 
     46 * <dl><dt><b>Source code:</b></dt> 
     47 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ome/OMEReader.java">Trac</a>, 
     48 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ome/OMEReader.java">SVN</a></dd></dl> 
    4549 */ 
    4650public class OMEReader extends FormatReader { 
  • trunk/loci/formats/ome/OMEWriter.java

    r3013 r3015  
    3434import org.openmicroscopy.is.*; 
    3535 
    36 /** Uploads images to an OME server. */ 
     36/** 
     37 * Uploads images to an OME server. 
     38 * 
     39 * <dl><dt><b>Source code:</b></dt> 
     40 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ome/OMEWriter.java">Trac</a>, 
     41 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ome/OMEWriter.java">SVN</a></dd></dl> 
     42 */ 
    3743public class OMEWriter extends FormatWriter { 
    3844 
  • trunk/loci/formats/ome/OMEXMLMetadataStore.java

    r3013 r3015  
    3939 * A utility class for constructing and manipulating OME-XML DOMs. It requires 
    4040 * the org.openmicroscopy.xml package to compile (part of ome-java.jar). 
     41 * 
     42 * <dl><dt><b>Source code:</b></dt> 
     43 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ome/OMEXMLMetadataStore.java">Trac</a>, 
     44 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ome/OMEXMLMetadataStore.java">SVN</a></dd></dl> 
    4145 * 
    4246 * @author Curtis Rueden ctrueden at wisc.edu 
     
    138142  /* @see loci.formats.MetadataRetrieve#getImageCount() */ 
    139143  public int getImageCount() { 
    140     return getNodeCount("Image");  
    141   } 
    142  
    143   /* @see loci.formats.MetadataRetrieve#getImageName(Integer) */  
     144    return getNodeCount("Image"); 
     145  } 
     146 
     147  /* @see loci.formats.MetadataRetrieve#getImageName(Integer) */ 
    144148  public String getImageName(Integer n) { 
    145149    int ndx = n == null ? 0 : n.intValue(); 
     
    147151  } 
    148152 
    149   /* @see loci.formats.MetadataRetrieve#getCreationDate(Integer) */  
     153  /* @see loci.formats.MetadataRetrieve#getCreationDate(Integer) */ 
    150154  public String getCreationDate(Integer n) { 
    151155    int ndx = n == null ? 0 : n.intValue(); 
     
    153157  } 
    154158 
    155   /* @see loci.formats.MetadataRetrieve#getDescription(Integer) */  
     159  /* @see loci.formats.MetadataRetrieve#getDescription(Integer) */ 
    156160  public String getDescription(Integer n) { 
    157161    int ndx = n == null ? 0 : n.intValue(); 
     
    181185    return getAttribute("Experimenter", "Email", ndx); 
    182186  } 
    183    
     187 
    184188  /* @see loci.formats.MetadataRetrieve#getInstitution(Integer) */ 
    185189  public String getInstitution(Integer n) { 
    186190    int ndx = n == null ? 0 : n.intValue(); 
    187     return getAttribute("Experimenter", "Institution", ndx);  
     191    return getAttribute("Experimenter", "Institution", ndx); 
    188192  } 
    189193 
     
    191195  public String getDataDirectory(Integer n) { 
    192196    int ndx = n == null ? 0 : n.intValue(); 
    193     return getAttribute("Experimenter", "DataDirectory", ndx);  
     197    return getAttribute("Experimenter", "DataDirectory", ndx); 
    194198  } 
    195199 
     
    197201  public Object getGroup(Integer n) { 
    198202    int ndx = n == null ? 0 : n.intValue(); 
    199     return getAttribute("Experimenter", "Group", ndx);  
     203    return getAttribute("Experimenter", "Group", ndx); 
    200204  } 
    201205 
    202206  /* @see loci.formats.MetadataRetrieve#getGroupCount() */ 
    203207  public int getGroupCount() { 
    204     return getNodeCount("Group");  
     208    return getNodeCount("Group"); 
    205209  } 
    206210 
     
    208212  public String getGroupName(Integer n) { 
    209213    int ndx = n == null ? 0 : n.intValue(); 
    210     return getAttribute("Group", "Name", ndx);  
     214    return getAttribute("Group", "Name", ndx); 
    211215  } 
    212216 
     
    214218  public Object getLeader(Integer n) { 
    215219    int ndx = n == null ? 0 : n.intValue(); 
    216     return getAttribute("Group", "Leader", ndx);  
     220    return getAttribute("Group", "Leader", ndx); 
    217221  } 
    218222 
     
    220224  public Object getContact(Integer n) { 
    221225    int ndx = n == null ? 0 : n.intValue(); 
    222     return getAttribute("Group", "Contact", ndx);  
     226    return getAttribute("Group", "Contact", ndx); 
    223227  } 
    224228 
    225229  /* @see loci.formats.MetadataRetrieve#getInstrumentCount() */ 
    226230  public int getInstrumentCount() { 
    227     return getNodeCount("Instrument");  
     231    return getNodeCount("Instrument"); 
    228232  } 
    229233 
     
    231235  public String getManufacturer(Integer n) { 
    232236    int ndx = n == null ? 0 : n.intValue(); 
    233     return getAttribute("Instrument", "Manufacturer", ndx);  
     237    return getAttribute("Instrument", "Manufacturer", ndx); 
    234238  } 
    235239 
     
    237241  public String getModel(Integer n) { 
    238242    int ndx = n == null ? 0 : n.intValue(); 
    239     return getAttribute("Instrument", "Model", ndx);  
     243    return getAttribute("Instrument", "Model", ndx); 
    240244  } 
    241245 
     
    243247  public String getSerialNumber(Integer n) { 
    244248    int ndx = n == null ? 0 : n.intValue(); 
    245     return getAttribute("Instrument", "SerialNumber", ndx);  
     249    return getAttribute("Instrument", "SerialNumber", ndx); 
    246250  } 
    247251 
     
    249253  public String getType(Integer n) { 
    250254    int ndx = n == null ? 0 : n.intValue(); 
    251     return getAttribute("Instrument", "Type", ndx);  
    252   } 
    253  
    254   /* @see loci.formats.MetadataRetrieve#getPixelSizeX(Integer) */  
     255    return getAttribute("Instrument", "Type", ndx); 
     256  } 
     257 
     258  /* @see loci.formats.MetadataRetrieve#getPixelSizeX(Integer) */ 
    255259  public Float getPixelSizeX(Integer n) { 
    256260    int ndx = n == null ? 0 : n.intValue(); 
     
    259263  } 
    260264 
    261   /* @see loci.formats.MetadataRetrieve#getPixelSizeY(Integer) */  
     265  /* @see loci.formats.MetadataRetrieve#getPixelSizeY(Integer) */ 
    262266  public Float getPixelSizeY(Integer n) { 
    263267    int ndx = n == null ? 0 : n.intValue(); 
     
    266270  } 
    267271 
    268   /* @see loci.formats.MetadataRetrieve#getPixelSizeZ(Integer) */  
     272  /* @see loci.formats.MetadataRetrieve#getPixelSizeZ(Integer) */ 
    269273  public Float getPixelSizeZ(Integer n) { 
    270274    int ndx = n == null ? 0 : n.intValue(); 
     
    273277  } 
    274278 
    275   /* @see loci.formats.MetadataRetrieve#getPixelSizeC(Integer) */  
     279  /* @see loci.formats.MetadataRetrieve#getPixelSizeC(Integer) */ 
    276280  public Float getPixelSizeC(Integer n) { 
    277281    int ndx = n == null ? 0 : n.intValue(); 
     
    280284  } 
    281285 
    282   /* @see loci.formats.MetadataRetrieve#getPixelSizeT(Integer) */  
     286  /* @see loci.formats.MetadataRetrieve#getPixelSizeT(Integer) */ 
    283287  public Float getPixelSizeT(Integer n) { 
    284288    int ndx = n == null ? 0 : n.intValue(); 
     
    289293  /* @see loci.formats.MetadataRetrieve#getDisplayROICount() */ 
    290294  public int getDisplayROICount() { 
    291     return getNodeCount("DisplayROI");  
     295    return getNodeCount("DisplayROI"); 
    292296  } 
    293297 
     
    295299  public Integer getX0(Integer n) { 
    296300    int ndx = n == null ? 0 : n.intValue(); 
    297     String x0 = getAttribute("DisplayROI", "X0", ndx);  
    298     return x0 == null ? null : new Integer(x0);  
     301    String x0 = getAttribute("DisplayROI", "X0", ndx); 
     302    return x0 == null ? null : new Integer(x0); 
    299303  } 
    300304 
     
    302306  public Integer getY0(Integer n) { 
    303307    int ndx = n == null ? 0 : n.intValue(); 
    304     String y0 = getAttribute("DisplayROI", "Y0", ndx);  
    305     return y0 == null ? null : new Integer(y0);  
     308    String y0 = getAttribute("DisplayROI", "Y0", ndx); 
     309    return y0 == null ? null : new Integer(y0); 
    306310  } 
    307311 
     
    309313  public Integer getZ0(Integer n) { 
    310314    int ndx = n == null ? 0 : n.intValue(); 
    311     String z0 = getAttribute("DisplayROI", "Z0", ndx);  
    312     return z0 == null ? null : new Integer(z0);  
     315    String z0 = getAttribute("DisplayROI", "Z0", ndx); 
     316    return z0 == null ? null : new Integer(z0); 
    313317  } 
    314318 
     
    316320  public Integer getT0(Integer n) { 
    317321    int ndx = n == null ? 0 : n.intValue(); 
    318     String t0 = getAttribute("DisplayROI", "T0", ndx);  
    319     return t0 == null ? null : new Integer(t0);  
     322    String t0 = getAttribute("DisplayROI", "T0", ndx); 
     323    return t0 == null ? null : new Integer(t0); 
    320324  } 
    321325 
     
    323327  public Integer getX1(Integer n) { 
    324328    int ndx = n == null ? 0 : n.intValue(); 
    325     String x1 = getAttribute("DisplayROI", "X1", ndx);  
    326     return x1 == null ? null : new Integer(x1);  
     329    String x1 = getAttribute("DisplayROI", "X1", ndx); 
     330    return x1 == null ? null : new Integer(x1); 
    327331  } 
    328332 
     
    330334  public Integer getY1(Integer n) { 
    331335    int ndx = n == null ? 0 : n.intValue(); 
    332     String y1 = getAttribute("DisplayROI", "Y1", ndx);  
    333     return y1 == null ? null : new Integer(y1);  
     336    String y1 = getAttribute("DisplayROI", "Y1", ndx); 
     337    return y1 == null ? null : new Integer(y1); 
    334338  } 
    335339 
     
    337341  public Integer getZ1(Integer n) { 
    338342    int ndx = n == null ? 0 : n.intValue(); 
    339     String z1 = getAttribute("DisplayROI", "Z1", ndx);  
    340     return z1 == null ? null : new Integer(z1);  
     343    String z1 = getAttribute("DisplayROI", "Z1", ndx); 
     344    return z1 == null ? null : new Integer(z1); 
    341345  } 
    342346 
     
    344348  public Integer getT1(Integer n) { 
    345349    int ndx = n == null ? 0 : n.intValue(); 
    346     String t1 = getAttribute("DisplayROI", "T1", ndx);  
    347     return t1 == null ? null : new Integer(t1);  
     350    String t1 = getAttribute("DisplayROI", "T1", ndx); 
     351    return t1 == null ? null : new Integer(t1); 
    348352  } 
    349353 
     
    351355  public Object getDisplayOptions(Integer n) { 
    352356    int ndx = n == null ? 0 : n.intValue(); 
    353     return getAttribute("DisplayROI", "DisplayOptions", ndx);  
     357    return getAttribute("DisplayROI", "DisplayOptions", ndx); 
    354358  } 
    355359 
    356360  /* @see loci.formats.MetadataRetrieve#getPixelsCount(Integer) */ 
    357361  public int getPixelsCount(Integer n) { 
    358     return getNodeCount("Image") / getNodeCount("Pixels");  
    359   } 
    360  
    361   /* @see loci.formats.MetadataRetrieve#getSizeX(Integer) */  
     362    return getNodeCount("Image") / getNodeCount("Pixels"); 
     363  } 
     364 
     365  /* @see loci.formats.MetadataRetrieve#getSizeX(Integer) */ 
    362366  public Integer getSizeX(Integer image) { 
    363367    int ndx = image == null ? 0 : image.intValue(); 
     
    366370  } 
    367371 
    368   /* @see loci.formats.MetadataRetrieve#getSizeY(Integer) */  
     372  /* @see loci.formats.MetadataRetrieve#getSizeY(Integer) */ 
    369373  public Integer getSizeY(Integer image) { 
    370374    int ndx = image == null ? 0 : image.intValue(); 
     
    373377  } 
    374378 
    375   /* @see loci.formats.MetadataRetrieve#getSizeZ(Integer) */  
     379  /* @see loci.formats.MetadataRetrieve#getSizeZ(Integer) */ 
    376380  public Integer getSizeZ(Integer image) { 
    377381    int ndx = image == null ? 0 : image.intValue(); 
     
    380384  } 
    381385 
    382   /* @see loci.formats.MetadataRetrieve#getSizeC(Integer) */  
     386  /* @see loci.formats.MetadataRetrieve#getSizeC(Integer) */ 
    383387  public Integer getSizeC(Integer image) { 
    384388    int ndx = image == null ? 0 : image.intValue(); 
     
    387391  } 
    388392 
    389   /* @see loci.formats.MetadataRetrieve#getSizeT(Integer) */  
     393  /* @see loci.formats.MetadataRetrieve#getSizeT(Integer) */ 
    390394  public Integer getSizeT(Integer image) { 
    391395    int ndx = image == null ? 0 : image.intValue(); 
     
    394398  } 
    395399 
    396   /* @see loci.formats.MetadataRetrieve#getPixelType(Integer) */  
     400  /* @see loci.formats.MetadataRetrieve#getPixelType(Integer) */ 
    397401  public String getPixelType(Integer image) { 
    398402    int ndx = image == null ? 0 : image.intValue(); 
     
    400404  } 
    401405 
    402   /* @see loci.formats.MetadataRetrieve#getBigEndian(Integer) */  
     406  /* @see loci.formats.MetadataRetrieve#getBigEndian(Integer) */ 
    403407  public Boolean getBigEndian(Integer image) { 
    404408    int ndx = image == null ? 0 : image.intValue(); 
     
    408412  } 
    409413 
    410   /* @see loci.formats.MetadataRetrieve#getDimensionOrder(Integer) */  
     414  /* @see loci.formats.MetadataRetrieve#getDimensionOrder(Integer) */ 
    411415  public String getDimensionOrder(Integer image) { 
    412416    int ndx = image == null ? 0 : image.intValue(); 
     
    416420  /* @see loci.formats.MetadataRetrieve#getStageLabelCount() */ 
    417421  public int getStageLabelCount() { 
    418     return getNodeCount("StageLabel");  
    419   } 
    420  
    421   /* @see loci.formats.MetadataRetrieve(Integer) */  
     422    return getNodeCount("StageLabel"); 
     423  } 
     424 
     425  /* @see loci.formats.MetadataRetrieve(Integer) */ 
    422426  public String getStageName(Integer n) { 
    423427    int ndx = n == null ? 0 : n.intValue(); 
     
    425429  } 
    426430 
    427   /* @see loci.formats.MetadataRetrieve(Integer) */  
     431  /* @see loci.formats.MetadataRetrieve(Integer) */ 
    428432  public Float getStageX(Integer n) { 
    429433    int ndx = n == null ? 0 : n.intValue(); 
     
    432436  } 
    433437 
    434   /* @see loci.formats.MetadataRetrieve(Integer) */  
     438  /* @see loci.formats.MetadataRetrieve(Integer) */ 
    435439  public Float getStageY(Integer n) { 
    436440    int ndx = n == null ? 0 : n.intValue(); 
     
    439443  } 
    440444 
    441   /* @see loci.formats.MetadataRetrieve(Integer) */  
     445  /* @see loci.formats.MetadataRetrieve(Integer) */ 
    442446  public Float getStageZ(Integer n) { 
    443447    int ndx = n == null ? 0 : n.intValue(); 
     
    450454    int ndx = n == null ? 0 : n.intValue(); 
    451455    ImageNode image = (ImageNode) getChild(root, "Image", ndx); 
    452     CustomAttributesNode ca =  
     456    CustomAttributesNode ca = 
    453457      (CustomAttributesNode) getChild(image, "CustomAttributes", 0); 
    454458    Vector v = DOMUtil.getChildElements("LogicalChannel", ca.getDOMElement()); 
     
    460464    int ndx = pixels == null ? 0 : pixels.intValue(); 
    461465    ImageNode image = (ImageNode) getChild(root, "Image", ndx); 
    462     CustomAttributesNode ca =  
     466    CustomAttributesNode ca = 
    463467      (CustomAttributesNode) getChild(image, "CustomAttributes", 0); 
    464     LogicalChannelNode ch = (LogicalChannelNode)  
    465       getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue());  
    466     return ch.getName();  
     468    LogicalChannelNode ch = (LogicalChannelNode) 
     469      getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue()); 
     470    return ch.getName(); 
    467471  } 
    468472 
     
    471475    int ndx = pixels == null ? 0 : pixels.intValue(); 
    472476    ImageNode image = (ImageNode) getChild(root, "Image", ndx); 
    473     CustomAttributesNode ca =  
     477    CustomAttributesNode ca = 
    474478      (CustomAttributesNode) getChild(image, "CustomAttributes", 0); 
    475     LogicalChannelNode ch = (LogicalChannelNode)  
    476       getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue());  
    477     return ch.getNDFilter();  
     479    LogicalChannelNode ch = (LogicalChannelNode) 
     480      getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue()); 
     481    return ch.getNDFilter(); 
    478482  } 
    479483 
     
    482486    int ndx = pixels == null ? 0 : pixels.intValue(); 
    483487    ImageNode image = (ImageNode) getChild(root, "Image", ndx); 
    484     CustomAttributesNode ca =  
     488    CustomAttributesNode ca = 
    485489      (CustomAttributesNode) getChild(image, "CustomAttributes", 0); 
    486     LogicalChannelNode ch = (LogicalChannelNode)  
    487       getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue());  
    488     return ch.getEmissionWavelength();  
     490    LogicalChannelNode ch = (LogicalChannelNode) 
     491      getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue()); 
     492    return ch.getEmissionWavelength(); 
    489493  } 
    490494 
     
    493497    int ndx = pixels == null ? 0 : pixels.intValue(); 
    494498    ImageNode image = (ImageNode) getChild(root, "Image", ndx); 
    495     CustomAttributesNode ca =  
     499    CustomAttributesNode ca = 
    496500      (CustomAttributesNode) getChild(image, "CustomAttributes", 0); 
    497     LogicalChannelNode ch = (LogicalChannelNode)  
    498       getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue());  
    499     return ch.getExcitationWavelength();  
    500   } 
    501  
    502   /**  
    503    * @see loci.formats.MetadataRetrieve#getPhotometricInterpretation(Integer,  
    504    * Integer)  
     501    LogicalChannelNode ch = (LogicalChannelNode) 
     502      getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue()); 
     503    return ch.getExcitationWavelength(); 
     504  } 
     505 
     506  /** 
     507   * @see loci.formats.MetadataRetrieve#getPhotometricInterpretation(Integer, 
     508   * Integer) 
    505509   */ 
    506510  public String getPhotometricInterpretation(Integer pixels, Integer channel) { 
    507511    int ndx = pixels == null ? 0 : pixels.intValue(); 
    508512    ImageNode image = (ImageNode) getChild(root, "Image", ndx); 
    509     CustomAttributesNode ca =  
     513    CustomAttributesNode ca = 
    510514      (CustomAttributesNode) getChild(image, "CustomAttributes", 0); 
    511     LogicalChannelNode ch = (LogicalChannelNode)  
    512       getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue());  
    513     return ch.getPhotometricInterpretation();  
     515    LogicalChannelNode ch = (LogicalChannelNode) 
     516      getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue()); 
     517    return ch.getPhotometricInterpretation(); 
    514518  } 
    515519 
     
    518522    int ndx = pixels == null ? 0 : pixels.intValue(); 
    519523    ImageNode image = (ImageNode) getChild(root, "Image", ndx); 
    520     CustomAttributesNode ca =  
     524    CustomAttributesNode ca = 
    521525      (CustomAttributesNode) getChild(image, "CustomAttributes", 0); 
    522     LogicalChannelNode ch = (LogicalChannelNode)  
    523       getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue());  
    524     return ch.getMode();  
     526    LogicalChannelNode ch = (LogicalChannelNode) 
     527      getChild(ca, "LogicalChannel", channel == null ? 0 : channel.intValue()); 
     528    return ch.getMode(); 
    525529  } 
    526530 
     
    539543  } 
    540544 
    541   /**  
    542    * @see loci.formats.MetadataRetrieve#getTimestamp(Integer, Integer,  
    543    * Integer, Integer)  
     545  /** 
     546   * @see loci.formats.MetadataRetrieve#getTimestamp(Integer, Integer, 
     547   * Integer, Integer) 
    544548   */ 
    545549  public Float getTimestamp(Integer pixels, Integer z, Integer c, Integer t) { 
     
    564568    return temperature == null ? null : new Float(temperature); 
    565569  } 
    566    
     570 
    567571  /* @see loci.formats.MetadataRetrieve#getAirPressure(Integer) */ 
    568572  public Float getAirPressure(Integer n) { 
     
    590594    int ndx = pixels == null ? 0 : pixels.intValue(); 
    591595    ImageNode image = (ImageNode) getChild(root, "Image", ndx); 
    592     CustomAttributesNode ca =  
     596    CustomAttributesNode ca = 
    593597      (CustomAttributesNode) getChild(image, "CustomAttributes", 0); 
    594     DisplayChannelNode display = (DisplayChannelNode)  
    595       getChild(ca, "DisplayChannel", channel == null ? 0 : channel.intValue());  
    596     return display.getBlackLevel();  
     598    DisplayChannelNode display = (DisplayChannelNode) 
     599      getChild(ca, "DisplayChannel", channel == null ? 0 : channel.intValue()); 
     600    return display.getBlackLevel(); 
    597601  } 
    598602 
     
    601605    int ndx = pixels == null ? 0 : pixels.intValue(); 
    602606    ImageNode image = (ImageNode) getChild(root, "Image", ndx); 
    603     CustomAttributesNode ca =  
     607    CustomAttributesNode ca = 
    604608      (CustomAttributesNode) getChild(image, "CustomAttributes", 0); 
    605     DisplayChannelNode display = (DisplayChannelNode)  
    606       getChild(ca, "DisplayChannel", channel == null ? 0 : channel.intValue());  
    607     return display.getWhiteLevel();  
     609    DisplayChannelNode display = (DisplayChannelNode) 
     610      getChild(ca, "DisplayChannel", channel == null ? 0 : channel.intValue()); 
     611    return display.getWhiteLevel(); 
    608612  } 
    609613 
     
    612616    int ndx = pixels == null ? 0 : pixels.intValue(); 
    613617    ImageNode image = (ImageNode) getChild(root, "Image", ndx); 
    614     CustomAttributesNode ca =  
     618    CustomAttributesNode ca = 
    615619      (CustomAttributesNode) getChild(image, "CustomAttributes", 0); 
    616     DisplayChannelNode display = (DisplayChannelNode)  
    617       getChild(ca, "DisplayChannel", channel == null ? 0 : channel.intValue());  
    618     return display.getGamma();  
     620    DisplayChannelNode display = (DisplayChannelNode) 
     621      getChild(ca, "DisplayChannel", channel == null ? 0 : channel.intValue()); 
     622    return display.getGamma(); 
    619623  } 
    620624 
     
    622626  public Float getZoom(Integer image) { 
    623627    int ndx = image == null ? 0 : image.intValue(); 
    624     String zoom = getAttribute("DisplayOptions", "Zoom", ndx);  
    625     return zoom == null ? null : new Float(zoom);  
     628    String zoom = getAttribute("DisplayOptions", "Zoom", ndx); 
     629    return zoom == null ? null : new Float(zoom); 
    626630  } 
    627631 
     
    629633  public Boolean isRedChannelOn(Integer image) { 
    630634    int ndx = image == null ? 0 : image.intValue(); 
    631     String redOn = getAttribute("DisplayOptions", "RedChannelOn", ndx);  
    632     return redOn == null ? null : new Boolean(redOn);  
     635    String redOn = getAttribute("DisplayOptions", "RedChannelOn", ndx); 
     636    return redOn == null ? null : new Boolean(redOn); 
    633637  } 
    634638 
     
    636640  public Boolean isGreenChannelOn(Integer image) { 
    637641    int ndx = image == null ? 0 : image.intValue(); 
    638     String greenOn = getAttribute("DisplayOptions", "GreenChannelOn", ndx);  
    639     return greenOn == null ? null : new Boolean(greenOn);  
     642    String greenOn = getAttribute("DisplayOptions", "GreenChannelOn", ndx); 
     643    return greenOn == null ? null : new Boolean(greenOn); 
    640644  } 
    641645 
     
    643647  public Boolean isBlueChannelOn(Integer image) { 
    644648    int ndx = image == null ? 0 : image.intValue(); 
    645     String blueOn = getAttribute("DisplayOptions", "BlueChannelOn", ndx);  
    646     return blueOn == null ? null : new Boolean(blueOn);  
     649    String blueOn = getAttribute("DisplayOptions", "BlueChannelOn", ndx); 
     650    return blueOn == null ? null : new Boolean(blueOn); 
    647651  } 
    648652 
     
    657661  public String getColorMap(Integer image) { 
    658662    int ndx = image == null ? 0 : image.intValue(); 
    659     return getAttribute("DisplayOptions", "ColorMap", ndx);  
     663    return getAttribute("DisplayOptions", "ColorMap", ndx); 
    660664  } 
    661665 
     
    673677    return zstop == null ? null : new Integer(zstop); 
    674678  } 
    675   
     679 
    676680  /* @see loci.formats.MetadataRetrieve#getTStart(Integer) */ 
    677681  public Integer getTStart(Integer image) { 
    678     int ndx = image == null ? 0 : image.intValue();  
     682    int ndx = image == null ? 0 : image.intValue(); 
    679683    String tstart = getAttribute("DisplayOptions", "TStart", ndx); 
    680684    return tstart == null ? null : new Integer(tstart); 
     
    683687  /* @see loci.formats.MetadataRetrieve#getTStop(Integer) */ 
    684688  public Integer getTStop(Integer image) { 
    685     int ndx = image == null ? 0 : image.intValue();  
     689    int ndx = image == null ? 0 : image.intValue(); 
    686690    String tstop = getAttribute("DisplayOptions", "TStop", ndx); 
    687691    return tstop == null ? null : new Integer(tstop); 
     
    722726    int ndx = laser == null ? 0 : laser.intValue(); 
    723727    String wave = getAttribute("Laser", "Wavelength", ndx); 
    724     return wave == null ? null : new Integer(wave);  
     728    return wave == null ? null : new Integer(wave); 
    725729  } 
    726730 
     
    729733    int ndx = laser == null ? 0 : laser.intValue(); 
    730734    String freq = getAttribute("Laser", "FrequencyDoubled", ndx); 
    731     return freq == null ? null : new Boolean(freq);  
     735    return freq == null ? null : new Boolean(freq); 
    732736  } 
    733737 
     
    736740    int ndx = laser == null ? 0 : laser.intValue(); 
    737741    String tunable = getAttribute("Laser", "Tunable", ndx); 
    738     return tunable == null ? null : new Boolean(tunable);  
     742    return tunable == null ? null : new Boolean(tunable); 
    739743  } 
    740744 
     
    749753    int ndx = laser == null ? 0 : laser.intValue(); 
    750754    String power = getAttribute("Laser", "Power", ndx); 
    751     return power == null ? null : new Float(power);  
     755    return power == null ? null : new Float(power); 
    752756  } 
    753757 
     
    762766    int ndx = filament == null ? 0 : filament.intValue(); 
    763767    String power = getAttribute("Filament", "Power", ndx); 
    764     return power == null ? null : new Float(power);  
     768    return power == null ? null : new Float(power); 
    765769  } 
    766770 
     
    775779    int ndx = arc == null ? 0 : arc.intValue(); 
    776780    String power = getAttribute("Arc", "Power", ndx); 
    777     return power == null ? null : new Float(power);  
     781    return power == null ? null : new Float(power); 
    778782  } 
    779783 
     
    806810    int ndx = detector == null ? 0 : detector.intValue(); 
    807811    String gain = getAttribute("Detector", "Gain", ndx); 
    808     return gain == null ? null : new Float(gain);  
    809   } 
    810    
     812    return gain == null ? null : new Float(gain); 
     813  } 
     814 
    811815  /* @see loci.formats.MetadataRetrieve#getDetectorVoltage(Integer) */ 
    812816  public Float getDetectorVoltage(Integer detector) { 
    813817    int ndx = detector == null ? 0 : detector.intValue(); 
    814818    String voltage = getAttribute("Detector", "Voltage", ndx); 
    815     return voltage == null ? null : new Float(voltage);  
     819    return voltage == null ? null : new Float(voltage); 
    816820  } 
    817821 
     
    820824    int ndx = detector == null ? 0 : detector.intValue(); 
    821825    String offset = getAttribute("Detector", "Offset", ndx); 
    822     return offset == null ? null : new Float(offset);  
     826    return offset == null ? null : new Float(offset); 
    823827  } 
    824828 
     
    833837    int ndx = objective == null ? 0 : objective.intValue(); 
    834838    return getAttribute("Objective", "Model", ndx); 
    835   }  
     839  } 
    836840 
    837841  /* @see loci.formats.MetadataRetrieve#getObjectiveSerial(Integer) */ 
     
    845849    int ndx = objective == null ? 0 : objective.intValue(); 
    846850    String na = getAttribute("Objective", "LensNA", ndx); 
    847     return na == null ? null : new Float(na);  
     851    return na == null ? null : new Float(na); 
    848852  } 
    849853 
     
    852856    int ndx = objective == null ? 0 : objective.intValue(); 
    853857    String mag = getAttribute("Objective", "Magnification", ndx); 
    854     return mag == null ? null : new Float(mag);  
     858    return mag == null ? null : new Float(mag); 
    855859  } 
    856860 
     
    941945  /* @see loci.formats.MetadataRetrieve#getOTFSizeX(Integer) */ 
    942946  public Integer getOTFSizeX(Integer otf) { 
    943     int ndx = otf == null ? 0 : otf.intValue();  
     947    int ndx = otf == null ? 0 : otf.intValue(); 
    944948    String x = getAttribute("OTF", "SizeX", ndx); 
    945949    return x == null ? null : new Integer(x); 
     
    948952  /* @see loci.formats.MetadataRetrieve#getOTFSizeY(Integer) */ 
    949953  public Integer getOTFSizeY(Integer otf) { 
    950     int ndx = otf == null ? 0 : otf.intValue();  
     954    int ndx = otf == null ? 0 : otf.intValue(); 
    951955    String y = getAttribute("OTF", "SizeY", ndx); 
    952956    return y == null ? null : new Integer(y); 
     
    955959  /* @see loci.formats.MetadataRetrieve#getOTFPixelType(Integer) */ 
    956960  public String getOTFPixelType(Integer otf) { 
    957     int ndx = otf == null ? 0 : otf.intValue();  
     961    int ndx = otf == null ? 0 : otf.intValue(); 
    958962    return getAttribute("OTF", "PixelType", ndx); 
    959963  } 
     
    961965  /* @see loci.formats.MetadataRetrieve#getOTFPath(Integer) */ 
    962966  public String getOTFPath(Integer otf) { 
    963     int ndx = otf == null ? 0 : otf.intValue();  
     967    int ndx = otf == null ? 0 : otf.intValue(); 
    964968    return getAttribute("OTF", "Path", ndx); 
    965969  } 
     
    967971  /* @see loci.formats.MetadataRetrieve#getOTFOpticalAxisAverage(Integer) */ 
    968972  public Boolean getOTFOpticalAxisAverage(Integer otf) { 
    969     int ndx = otf == null ? 0 : otf.intValue();  
     973    int ndx = otf == null ? 0 : otf.intValue(); 
    970974    String x = getAttribute("OTF", "SizeX", ndx); 
    971975    return x == null ? null : new Boolean(x); 
     
    17801784    Element rel = root.getDOMElement(); 
    17811785    Vector elements = DOMUtil.findElementList(name, rel.getOwnerDocument()); 
    1782     return elements.size();  
     1786    return elements.size(); 
    17831787  } 
    17841788 
  • trunk/loci/formats/ome/OmeisException.java

    r2327 r3015  
    2828 * OmeisException is the exception thrown when something 
    2929 * goes wrong performing a file format operation. 
     30 * 
     31 * <dl><dt><b>Source code:</b></dt> 
     32 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ome/OmeisException.java">Trac</a>, 
     33 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ome/OmeisException.java">SVN</a></dd></dl> 
    3034 */ 
    3135public class OmeisException extends Exception { 
  • trunk/loci/formats/ome/OmeisImporter.java

    r2762 r3015  
    3636/** 
    3737 * A command line utility used by OMEIS to interface with Bio-Formats. 
     38 * 
     39 * <dl><dt><b>Source code:</b></dt> 
     40 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/ome/OmeisImporter.java">Trac</a>, 
     41 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/ome/OmeisImporter.java">SVN</a></dd></dl> 
    3842 * 
    3943 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/out/AVIWriter.java

    r2687 r3015  
    3737 * AVI Movie Writer plugin for ImageJ 
    3838 * (available at http://rsb.info.nih.gov/ij/). 
     39 * 
     40 * <dl><dt><b>Source code:</b></dt> 
     41 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/out/AVIWriter.java">Trac</a>, 
     42 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/out/AVIWriter.java">SVN</a></dd></dl> 
    3943 */ 
    4044public class AVIWriter extends FormatWriter { 
  • trunk/loci/formats/out/EPSWriter.java

    r2687 r3015  
    3232/** 
    3333 * EPSWriter is the file format writer for Encapsulated PostScript (EPS) files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/out/EPSWriter.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/out/EPSWriter.java">SVN</a></dd></dl> 
    3438 * 
    3539 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/out/ImageIOWriter.java

    r2687 r3015  
    3737 * ImageIOWriter is the superclass for file format writers that use the 
    3838 * javax.imageio library. 
     39 * 
     40 * <dl><dt><b>Source code:</b></dt> 
     41 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/out/ImageIOWriter.java">Trac</a>, 
     42 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/out/ImageIOWriter.java">SVN</a></dd></dl> 
    3943 * 
    4044 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/out/JPEGWriter.java

    r2687 r3015  
    3030import loci.formats.*; 
    3131 
    32 /** JPEGWriter is the file format writer for JPEG files. */ 
     32/** 
     33 * JPEGWriter is the file format writer for JPEG files. 
     34 * 
     35 * <dl><dt><b>Source code:</b></dt> 
     36 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/out/JPEGWriter.java">Trac</a>, 
     37 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/out/JPEGWriter.java">SVN</a></dd></dl> 
     38 */ 
    3339public class JPEGWriter extends ImageIOWriter { 
    3440 
  • trunk/loci/formats/out/LegacyQTWriter.java

    r2857 r3015  
    3737 * Much of this code was based on the QuickTime Movie Writer for ImageJ 
    3838 * (available at http://rsb.info.nih.gov/ij/plugins/movie-writer.html). 
     39 * 
     40 * <dl><dt><b>Source code:</b></dt> 
     41 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/out/LegacyQTWriter.java">Trac</a>, 
     42 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/out/LegacyQTWriter.java">SVN</a></dd></dl> 
    3943 */ 
    4044public class LegacyQTWriter extends FormatWriter { 
  • trunk/loci/formats/out/OMETiffWriter.java

    r3013 r3015  
    2929import loci.formats.*; 
    3030 
    31 /** OMETiffWriter is the file format writer for OME-TIFF files. */ 
     31/** 
     32 * OMETiffWriter is the file format writer for OME-TIFF files. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/out/OMETiffWriter.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/out/OMETiffWriter.java">SVN</a></dd></dl> 
     37 */ 
    3238public class OMETiffWriter extends TiffWriter { 
    3339 
     
    3541 
    3642  public OMETiffWriter() { 
    37     super("OME-TIFF", new String[] {"ome.tif", "ome.tiff"});  
     43    super("OME-TIFF", new String[] {"ome.tif", "ome.tiff"}); 
    3844  } 
    3945 
    4046  // -- IFormatHandler API methods -- 
    4147 
    42   /* @see loci.formats.IFormatHandler#close() */  
    43   public void close() throws IOException {   
     48  /* @see loci.formats.IFormatHandler#close() */ 
     49  public void close() throws IOException { 
    4450    if (out != null) out.close(); 
    4551    out = null; 
    4652    if (currentId != null && retrieve != null) { 
    47       // write OME-XML to the first IFD's comment   
    48      
     53      // write OME-XML to the first IFD's comment 
     54 
    4955      MetadataStore omexml = null; 
    5056 
     
    5258        Class c = Class.forName("loci.formats.ome.OMEXMLMetadataStore"); 
    5359        omexml = (MetadataStore) c.newInstance(); 
    54       
    55         if (c.isInstance(retrieve)) omexml = (MetadataStore) retrieve;  
     60 
     61        if (c.isInstance(retrieve)) omexml = (MetadataStore) retrieve; 
    5662        else FormatTools.convertMetadata(retrieve, omexml); 
    57        
     63 
    5864        Method m = omexml.getClass().getMethod("dumpXML", (Class[]) null); 
    5965        String xml = (String) m.invoke(omexml, (Object[]) null); 
    60          
    61         // insert TiffData element  
     66 
     67        // insert TiffData element 
    6268        int pix = xml.indexOf("<Pixels "); 
    6369        int end = xml.indexOf("/>", pix); 
    64         xml = xml.substring(0, end) + "><TiffData/></Pixels>" +  
     70        xml = xml.substring(0, end) + "><TiffData/></Pixels>" + 
    6571          xml.substring(end + 2); 
    6672 
     
    7177      } 
    7278    } 
    73     super.close();  
     79    super.close(); 
    7480  } 
    7581 
  • trunk/loci/formats/out/PNGWriter.java

    r2687 r3015  
    2525package loci.formats.out; 
    2626 
    27 /** PNGWriter is the file format writer for PNG files. */ 
     27/** 
     28 * PNGWriter is the file format writer for PNG files. 
     29 * 
     30 * <dl><dt><b>Source code:</b></dt> 
     31 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/out/PNGWriter.java">Trac</a>, 
     32 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/out/PNGWriter.java">SVN</a></dd></dl> 
     33 */ 
    2834public class PNGWriter extends ImageIOWriter { 
    2935 
  • trunk/loci/formats/out/QTWriter.java

    r2687 r3015  
    3333/** 
    3434 * QTWriter is the file format writer for uncompressed QuickTime movie files. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/out/QTWriter.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/out/QTWriter.java">SVN</a></dd></dl> 
    3539 * 
    3640 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/loci/formats/out/TiffWriter.java

    r3013 r3015  
    3131import loci.formats.*; 
    3232 
    33 /** TiffWriter is the file format writer for TIFF files. */ 
     33/** 
     34 * TiffWriter is the file format writer for TIFF files. 
     35 * 
     36 * <dl><dt><b>Source code:</b></dt> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/out/TiffWriter.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/out/TiffWriter.java">SVN</a></dd></dl> 
     39 */ 
    3440public class TiffWriter extends FormatWriter { 
    3541 
     
    5460    super(format, exts); 
    5561    lastOffset = 0; 
    56     compressionTypes = new String[] {"Uncompressed", "LZW"};  
     62    compressionTypes = new String[] {"Uncompressed", "LZW"}; 
    5763  } 
    5864 
     
    7581   * The IFD hashtable allows specification of TIFF parameters such as bit 
    7682   * depth, compression and units. If this image is the last one in the series, 
    77    * the lastInSeries flag must be set. If this image is the last one in the  
     83   * the lastInSeries flag must be set. If this image is the last one in the 
    7884   * file, the last flag must be set. 
    7985   */ 
    80   public void saveImage(Image image, Hashtable ifd, int series,  
     86  public void saveImage(Image image, Hashtable ifd, int series, 
    8187    boolean lastInSeries, boolean last) throws IOException, FormatException 
    8288  { 
     
    122128 
    123129  /* @see loci.formats.IFormatWriter#saveImage(Image, boolean) */ 
    124   public void saveImage(Image image, boolean last)  
    125     throws FormatException, IOException  
     130  public void saveImage(Image image, boolean last) 
     131    throws FormatException, IOException 
    126132  { 
    127133    saveImage(image, 0, last, last); 
     
    129135 
    130136  /* @see loci.formats.IFormatWriter#saveImage(Image, int, boolean, boolean) */ 
    131   public void saveImage(Image image, int series, boolean lastInSeries,  
     137  public void saveImage(Image image, int series, boolean lastInSeries, 
    132138    boolean last) throws FormatException, IOException 
    133139  { 
  • trunk/loci/formats/test/ConfigurationFiles.java

    r2976 r3015  
    2929import loci.formats.*; 
    3030 
    31 /** Stores data from a set of config files. */ 
     31/** 
     32 * Stores data from a set of config files. 
     33 * 
     34 * <dl><dt><b>Source code:</b></dt> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/test/ConfigurationFiles.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/test/ConfigurationFiles.java">SVN</a></dd></dl> 
     37 */ 
    3238public class ConfigurationFiles { 
    3339 
  • trunk/loci/formats/test/ImageTester.java

    r2857 r3015  
    3535/** 
    3636 * A class for testing the ImageTools.makeImage methods. 
     37 * 
     38 * <dl><dt><b>Source code:</b></dt> 
     39 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/test/ImageTester.java">Trac</a>, 
     40 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/test/ImageTester.java">SVN</a></dd></dl> 
    3741 * 
    3842 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/test/ReaderTest.java

    r3013 r3015  
    3939 * java -ea -mx512m -Dtestng.directory="/path/" -Dtestng.multiplier="1.0" \ 
    4040 *   org.testng.TestNG -sourcedir . testng.xml 
     41 * 
     42 * <dl><dt><b>Source code:</b></dt> 
     43 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/test/ReaderTest.java">Trac</a>, 
     44 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/test/ReaderTest.java">SVN</a></dd></dl> 
    4145 */ 
    4246public class ReaderTest { 
     
    290294        boolean failC = reader.getSizeC() != store.getSizeC(ii).intValue(); 
    291295        boolean failT = reader.getSizeT() != store.getSizeT(ii).intValue(); 
    292         boolean failBE = reader.isLittleEndian() ==  
     296        boolean failBE = reader.isLittleEndian() == 
    293297          store.getBigEndian(ii).booleanValue(); 
    294298        boolean failDE = 
  • trunk/loci/ome/editor/ClickableList.java

    r2522 r3015  
    5050 * with the GUI of a NotePanel. 
    5151 * 
     52 * <dl><dt><b>Source code:</b></dt> 
     53 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/ome/editor/ClickableList.java">Trac</a>, 
     54 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/ome/editor/ClickableList.java">SVN</a></dd></dl> 
     55 * 
    5256 * @author Christopher Peterson crpeterson2 at wisc.edu 
    5357 */ 
  • trunk/loci/ome/editor/ClickableTable.java

    r2522 r3015  
    5757 * on the attributes being manipulated. 
    5858 * 
     59 * <dl><dt><b>Source code:</b></dt> 
     60 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/ome/editor/ClickableTable.java">Trac</a>, 
     61 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/ome/editor/ClickableTable.java">SVN</a></dd></dl> 
     62 * 
    5963 * @author Christopher Peterson crpeterson2 at wisc.edu 
    6064 */ 
  • trunk/loci/ome/editor/ExportDialog.java

    r2522 r3015  
    3737 * Note that much of this code was found in an example in 
    3838 * the JDK 1.4 API Specs... ListDialog.java . 
     39 * 
     40 * <dl><dt><b>Source code:</b></dt> 
     41 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/ome/editor/ExportDialog.java">Trac</a>, 
     42 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/ome/editor/ExportDialog.java">SVN</a></dd></dl> 
    3943 * 
    4044 * @author Christopher Peterson crpeterson2 at wisc.edu 
  • trunk/loci/ome/editor/MetadataEditor.java

    r2763 r3015  
    4040/** 
    4141 * An user-friendly application for displaying and editing OME-XML metadata. 
     42 * 
     43 * <dl><dt><b>Source code:</b></dt> 
     44 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/ome/editor/MetadataEditor.java">Trac</a>, 
     45 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/ome/editor/MetadataEditor.java">SVN</a></dd></dl> 
    4246 * 
    4347 * @author Christopher Peterson crpeterson2 at wisc.edu 
  • trunk/loci/ome/editor/MetadataPane.java

    r2763 r3015  
    5151 * Sadly you lose quite a bit of functionality such as the 
    5252 * various views if you choose to directly instatiate. 
     53 * 
     54 * <dl><dt><b>Source code:</b></dt> 
     55 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/ome/editor/MetadataPane.java">Trac</a>, 
     56 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/ome/editor/MetadataPane.java">SVN</a></dd></dl> 
    5357 * 
    5458 * @author Christopher Peterson crpeterson2 at wisc.edu 
  • trunk/loci/ome/editor/NotePane.java

    r2522 r3015  
    4848 * notes added to a particular OMEXML File by using the 
    4949 * preexisting NotePanels made by MetadataPane. 
     50 * 
     51 * <dl><dt><b>Source code:</b></dt> 
     52 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/ome/editor/NoteP